{ "extraArgs": { "biocVersion": "3.21" }, "packages": { "ABSSeq": { "name": "ABSSeq", "version": "1.62.0", "sha256": "11fkdzgm480qmyi9hscc99d0agdjvija01226np2s8k45iy4j0r8", "depends": ["limma", "locfit"] }, "ABarray": { "name": "ABarray", "version": "1.76.0", "sha256": "0rs6x9ccw3i5xzsinajqq300jxwp9v69s96wp1xdgpdx24azmq03", "depends": ["Biobase", "multtest"] }, "ACE": { "name": "ACE", "version": "1.26.0", "sha256": "0v78djw83b253gsjxs3m5ihxyz82gzvsqhbiblxcryvghzv1c7x3", "depends": ["Biobase", "GenomicRanges", "QDNAseq", "ggplot2"] }, "ACME": { "name": "ACME", "version": "2.64.0", "sha256": "1s1s00b6mrv710x14vnscs99iinqq5pml684vpgbshlvszzyw71h", "depends": ["Biobase", "BiocGenerics"] }, "ADAM": { "name": "ADAM", "version": "1.24.0", "sha256": "03258gs13spyg807ky217y4mv265cklykb8a6qvn2b9shyjss8qb", "depends": ["DT", "GO_db", "KEGGREST", "Rcpp", "SummarizedExperiment", "dplyr", "knitr", "pbapply", "stringr"] }, "ADAMgui": { "name": "ADAMgui", "version": "1.24.0", "sha256": "008ak7x5ph841ls60jzhycyyqkbqzvdj5px8nn1ig2if72krhhdw", "depends": ["ADAM", "DT", "GO_db", "RColorBrewer", "colorRamps", "data_table", "dplyr", "ggplot2", "ggpubr", "ggrepel", "ggsignif", "gridExtra", "knitr", "reshape2", "shiny", "shinyjs", "stringi", "stringr", "testthat", "varhandle"] }, "ADAPT": { "name": "ADAPT", "version": "1.2.0", "sha256": "0v4vivxvsfwxs1sds3lawsbjb7ajv769i3xqiqir29ifn6lsjlw1", "depends": ["Rcpp", "RcppArmadillo", "RcppParallel", "ggplot2", "ggrepel", "phyloseq"] }, "ADImpute": { "name": "ADImpute", "version": "1.18.0", "sha256": "0fa03prsxbwhqhhglr0c4fjgasa9g32i5fh73lc82axd86nk2vk3", "depends": ["BiocParallel", "DrImpute", "MASS", "Matrix", "S4Vectors", "SAVER", "SingleCellExperiment", "SummarizedExperiment", "checkmate", "data_table", "kernlab", "rsvd"] }, "ADaCGH2": { "name": "ADaCGH2", "version": "2.48.0", "sha256": "1wxqwd8grmn900qib8xxfvmfb2g2r8ic6rmc6nbqlpzgfq0aa325", "depends": ["DNAcopy", "aCGH", "bit", "cluster", "ff", "tilingArray", "waveslim"] }, "AGDEX": { "name": "AGDEX", "version": "1.56.0", "sha256": "14ykvs8rgf8c6gar5xacypsk2m30w4a8r3jmkdx1v3wxl510pbzk", "depends": ["Biobase", "GSEABase"] }, "AHMassBank": { "name": "AHMassBank", "version": "1.8.0", "sha256": "0iqf86vfff3rnxxchha5dp1fglnw13awpy703adlwasr7dx61sf4", "depends": ["AnnotationHubData"] }, "AIMS": { "name": "AIMS", "version": "1.40.0", "sha256": "0414w398wlr8rzcc9nyz3nq2xni5582p99i4d0bqydg35zdmzxr5", "depends": ["Biobase", "e1071"] }, "ALDEx2": { "name": "ALDEx2", "version": "1.40.0", "sha256": "1dblf8cabwy2jwi70v6l5n2fjjfpnxy6qdszs4klq152g2wnx3sg", "depends": ["BiocParallel", "GenomicRanges", "IRanges", "Rfast", "S4Vectors", "SummarizedExperiment", "directlabels", "lattice", "latticeExtra", "multtest", "zCompositions"] }, "AMARETTO": { "name": "AMARETTO", "version": "1.24.0", "sha256": "0njf8xm4z4s9gyyv8zybi9w4hzvv52i6wkspd7pd71k4m0xnpd33", "depends": ["BiocFileCache", "ComplexHeatmap", "DT", "Matrix", "MultiAssayExperiment", "Rcpp", "callr", "circlize", "curatedTCGAData", "doParallel", "dplyr", "foreach", "ggplot2", "glmnet", "gridExtra", "httr", "impute", "knitr", "limma", "matrixStats", "readr", "reshape2", "rmarkdown", "tibble"] }, "AMOUNTAIN": { "name": "AMOUNTAIN", "version": "1.34.0", "sha256": "1kqlbjzcp3hgp2v54v5jp34q19cb46s4g0cya7pkgk729b8wglz3", "depends": [] }, "ANCOMBC": { "name": "ANCOMBC", "version": "2.10.1", "sha256": "16cfr7q1ivksmajrfx5gv75z83aza443lw11as2nf8pbsfjwfgrf", "depends": ["CVXR", "DescTools", "Hmisc", "MASS", "Matrix", "Rdpack", "doParallel", "doRNG", "energy", "foreach", "gtools", "lme4", "lmerTest", "multcomp", "nloptr"] }, "ANF": { "name": "ANF", "version": "1.30.0", "sha256": "17rw1sb6fvan37hvsiv21zbldq7ajkxaxaswynjp33klycqkxvaf", "depends": ["Biobase", "MASS", "RColorBrewer", "igraph", "survival"] }, "APAlyzer": { "name": "APAlyzer", "version": "1.22.0", "sha256": "00a3barcm8yr4q7c9irpmg5v6v8ybzb2ww9mb1r7fdkg0kpj6dj9", "depends": ["DESeq2", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "HybridMTest", "Rsamtools", "Rsubread", "SummarizedExperiment", "VariantAnnotation", "dplyr", "ggplot2", "ggrepel", "repmis", "rtracklayer", "tidyr"] }, "APL": { "name": "APL", "version": "1.12.0", "sha256": "03s5aw0ij06rih2yqwp2flv1f943lkz0i0n00vr6maw6bpbzf19p", "depends": ["Matrix", "RSpectra", "SeuratObject", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "ggrepel", "magrittr", "org_Hs_eg_db", "org_Mm_eg_db", "plotly", "rlang", "topGO", "viridisLite"] }, "ARRmNormalization": { "name": "ARRmNormalization", "version": "1.48.0", "sha256": "0rgmi5rxv1qlgsdgbixcyabx8qpaai3f8pcv99pbnhby99m20ns4", "depends": ["ARRmData"] }, "ASAFE": { "name": "ASAFE", "version": "1.34.0", "sha256": "1hx8zxsbva755y5kj5s9jvwjjf84w27m2p0798r1byi69c1rqigd", "depends": [] }, "ASEB": { "name": "ASEB", "version": "1.52.0", "sha256": "19cvciadpjn0zjlh2bcrhsvwn1vzfm0rcxx89z6rw29hk0j98xgk", "depends": [] }, "ASGSCA": { "name": "ASGSCA", "version": "1.42.0", "sha256": "0d45hlz7445c1dxxbxlmjak87i8l33pxiyzjdpw78rshy9dz7910", "depends": ["MASS", "Matrix"] }, "ASICS": { "name": "ASICS", "version": "2.24.0", "sha256": "173v75sl33saf5ghmq610l6138p5wqy58xlzdlin7w6p8jl13yqc", "depends": ["BiocParallel", "Matrix", "PepsNMR", "SummarizedExperiment", "ggplot2", "glmnet", "gridExtra", "mvtnorm", "plyr", "quadprog", "ropls", "zoo"] }, "ASSET": { "name": "ASSET", "version": "2.26.0", "sha256": "04xnggnfvi5v9mcc3sbjq8prwz4acnvzg44fc3a9sa1fv51y5v7b", "depends": ["MASS", "msm", "rmeta"] }, "ASSIGN": { "name": "ASSIGN", "version": "1.44.0", "sha256": "1sfy9bqq4b7yljihn4kgc46rx5shy4lwyf0wxrjlcndrc29myhk9", "depends": ["Rlab", "ggplot2", "gplots", "msm", "sva", "yaml"] }, "ASURAT": { "name": "ASURAT", "version": "1.12.0", "sha256": "0wx54jf44i6qy7q46dki7pjdkmddq9zvzjj1v0s2izhr73xgrrfw", "depends": ["ComplexHeatmap", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "circlize", "cluster", "plot3D"] }, "ASpli": { "name": "ASpli", "version": "2.18.0", "sha256": "1v2a3kspr4xl7rr94jy7ldmdhh6px0817di6i7rq07vjpwsy29fx", "depends": ["AnnotationDbi", "BiocGenerics", "BiocStyle", "DT", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "MASS", "Rsamtools", "S4Vectors", "UpSetR", "data_table", "edgeR", "htmltools", "igraph", "limma", "pbmcapply", "tidyr", "txdbmaker"] }, "ATACseqQC": { "name": "ATACseqQC", "version": "1.32.0", "sha256": "04dnvjwxq64ax9d6mg5j30285wv1kc0yq7ms3m1bj6654v1vvpcq", "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "ChIPpeakAnno", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "GenomicScores", "IRanges", "KernSmooth", "Rsamtools", "S4Vectors", "edgeR", "limma", "motifStack", "preseqR", "randomForest", "rtracklayer"] }, "ATACseqTFEA": { "name": "ATACseqTFEA", "version": "1.10.0", "sha256": "1q7skafrkqwbkr8prkgglli18f0h76x4z0bqmmq1hcaw1l5zl4b2", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Matrix", "Rsamtools", "S4Vectors", "SummarizedExperiment", "TFBSTools", "dplyr", "ggplot2", "ggrepel", "limma", "motifmatchr", "pracma", "rtracklayer"] }, "AUCell": { "name": "AUCell", "version": "1.30.1", "sha256": "0wksn7l5g5k6cm3y1c4gsjrc37zf73w6nbzcdqb3p93lmnyk2dh2", "depends": ["BiocGenerics", "DelayedArray", "DelayedMatrixStats", "GSEABase", "Matrix", "R_utils", "SummarizedExperiment", "data_table", "mixtools"] }, "AWFisher": { "name": "AWFisher", "version": "1.22.0", "sha256": "181zy3kzx2kwirlk7kv3c4xph7frxs5z1imj76sbzgc13nsbf668", "depends": ["edgeR", "limma"] }, "AffiXcan": { "name": "AffiXcan", "version": "1.26.0", "sha256": "19h4cd2j9sv9nlj9d46sgd6rbi92vr3kp3qr6pd016rdj8an7inm", "depends": ["BiocParallel", "MultiAssayExperiment", "SummarizedExperiment", "crayon"] }, "AffyRNADegradation": { "name": "AffyRNADegradation", "version": "1.54.0", "sha256": "1sq5mawmykd14vvw6854mdpdc8qqn52l3z131by79j1sklbjah0d", "depends": ["affy"] }, "AgiMicroRna": { "name": "AgiMicroRna", "version": "2.58.0", "sha256": "1fqslyiwl3d9i2qvvhispf5g340vsl7wd2z61lfjw43p0azjlr1m", "depends": ["Biobase", "affy", "affycoretools", "limma", "preprocessCore"] }, "AllelicImbalance": { "name": "AllelicImbalance", "version": "1.46.1", "sha256": "1v20sw834khccr5x77q1wb6d9dk4w0hsfk994z34yx61p8wm6wqx", "depends": ["AnnotationDbi", "BSgenome", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "gridExtra", "lattice", "latticeExtra", "nlme", "seqinr"] }, "AlphaBeta": { "name": "AlphaBeta", "version": "1.22.0", "sha256": "04420pnxgnsba1jd1ma6cg889mmh2vs2c5p8570r3hxsgppzk6pj", "depends": ["BiocParallel", "data_table", "dplyr", "expm", "ggplot2", "gtools", "igraph", "optimx", "plotly", "stringr"] }, "AlphaMissenseR": { "name": "AlphaMissenseR", "version": "1.4.2", "sha256": "0q608p7mj57xi4g1n1wk00pmc5qb39acc7s4wbr9ckfsp3m8v8av", "depends": ["BiocBaseUtils", "BiocFileCache", "DBI", "curl", "dplyr", "duckdb", "ggplot2", "memoise", "rjsoncons", "rlang", "spdl", "whisker"] }, "AlpsNMR": { "name": "AlpsNMR", "version": "4.10.0", "sha256": "10d7q245crfvnx4rlsg879vchia35wnv9swsjbyqfbq3cvix4n0v", "depends": ["BiocParallel", "baseline", "cli", "dplyr", "fs", "generics", "ggplot2", "glue", "htmltools", "magrittr", "matrixStats", "mixOmics", "pcaPP", "purrr", "readxl", "reshape2", "rlang", "rmarkdown", "scales", "signal", "speaq", "stringr", "tibble", "tidyr", "tidyselect", "vctrs"] }, "AnVIL": { "name": "AnVIL", "version": "1.20.3", "sha256": "1sxhfp0h2ffaasjcpaw6lcr5msxk4bpz93c95yis724b7qmq341r", "depends": ["AnVILBase", "BiocBaseUtils", "DT", "dplyr", "futile_logger", "htmltools", "httr", "jsonlite", "miniUI", "rapiclient", "rlang", "shiny", "tibble", "tidyr", "tidyselect", "yaml"] }, "AnVILAz": { "name": "AnVILAz", "version": "1.2.0", "sha256": "02v9qn6nfc7gb1iqcwpaxnp66gqq0fyxm74a905xadnsp1c8z60j", "depends": ["AnVILBase", "BiocBaseUtils", "curl", "httr2", "jsonlite", "rjsoncons", "tibble"] }, "AnVILBase": { "name": "AnVILBase", "version": "1.2.0", "sha256": "1mia9qji8x8zs4h7m2vf3x4dhyarpxydn42zdfs0qmfiaq5lsrwk", "depends": ["dplyr", "httr", "httr2", "jsonlite", "tibble"] }, "AnVILBilling": { "name": "AnVILBilling", "version": "1.18.0", "sha256": "0xxkm92vxk8gq8hn4vjnmivxnxcfnybrls4wqwci7y6yn01s9vq0", "depends": ["DBI", "DT", "bigrquery", "dplyr", "ggplot2", "lubridate", "magrittr", "plotly", "shiny", "shinytoastr"] }, "AnVILGCP": { "name": "AnVILGCP", "version": "1.2.0", "sha256": "16msp62ifvazaz5c8vlr80fz2ds9rgf5rmng4phbv7isamh3h9sj", "depends": ["AnVILBase", "BiocBaseUtils", "dplyr", "httr", "jsonlite", "rlang", "tibble", "tidyr"] }, "AnVILPublish": { "name": "AnVILPublish", "version": "1.18.0", "sha256": "1rdabz5mxvsz8yqj39r4fskv201qm0dm1n984h9q4qwykj18w2xa", "depends": ["AnVIL", "AnVILGCP", "BiocBaseUtils", "BiocManager", "httr", "jsonlite", "readr", "rmarkdown", "whisker", "yaml"] }, "AnVILWorkflow": { "name": "AnVILWorkflow", "version": "1.8.0", "sha256": "0k31j6dlfkk7a8kdcvffb54rk0q19p6gicjmaxld9nlmr4527iid", "depends": ["AnVIL", "AnVILBase", "AnVILGCP", "dplyr", "httr", "jsonlite", "plyr", "rlang", "stringr", "tibble", "tidyr"] }, "Anaquin": { "name": "Anaquin", "version": "2.32.0", "sha256": "09f1pfy06jzhwbxjvh126yxnahk3y6hmcy5793wxnpgsy6wmmabl", "depends": ["DESeq2", "ROCR", "ggplot2", "knitr", "locfit", "plyr", "qvalue"] }, "AneuFinder": { "name": "AneuFinder", "version": "1.35.0", "sha256": "0zx0brvcyi9id7xli9h5nk9an7j46p7zgjj3qmwr3jm4b95qahpl", "depends": ["AneuFinderData", "BiocGenerics", "Biostrings", "DNAcopy", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "bamsignals", "cowplot", "doParallel", "ecp", "foreach", "ggdendro", "ggplot2", "ggrepel", "mclust", "reshape2"] }, "AnnotationDbi": { "name": "AnnotationDbi", "version": "1.70.0", "sha256": "1nx9yrj76gwxqi2v7ynp8z6p4zm8gc3dqqpn62akflcymc213ppq", "depends": ["Biobase", "BiocGenerics", "DBI", "IRanges", "KEGGREST", "RSQLite", "S4Vectors"] }, "AnnotationFilter": { "name": "AnnotationFilter", "version": "1.32.0", "sha256": "1r642f9qh8gxj5fypkkdav738s875minsyaz1qw4gi2ckv2j8jks", "depends": ["GenomicRanges", "lazyeval"] }, "AnnotationForge": { "name": "AnnotationForge", "version": "1.50.0", "sha256": "1h0h9axlq9knw8hiyhay7d9wbxvlgg8378pd6zygbj74qvy60pp3", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "DBI", "RCurl", "RSQLite", "S4Vectors", "XML"] }, "AnnotationHub": { "name": "AnnotationHub", "version": "3.16.1", "sha256": "16iw33kbkrbla9srj837ib458ddx2zaafinjya9xs27awhxdpc4p", "depends": ["AnnotationDbi", "BiocFileCache", "BiocGenerics", "BiocManager", "BiocVersion", "RSQLite", "S4Vectors", "curl", "dplyr", "httr", "rappdirs", "yaml"] }, "AnnotationHubData": { "name": "AnnotationHubData", "version": "1.38.0", "sha256": "17ajnm8ynd8v7n0fb99317kd5s80pzrjzcf1xhhmnqxf5hk8rk2m", "depends": ["AnnotationDbi", "AnnotationForge", "AnnotationHub", "Biobase", "BiocCheck", "BiocGenerics", "BiocManager", "Biostrings", "DBI", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "OrganismDbi", "RCurl", "RSQLite", "Rsamtools", "S4Vectors", "XML", "biocViews", "futile_logger", "graph", "jsonlite", "rtracklayer"] }, "ArrayExpress": { "name": "ArrayExpress", "version": "1.68.0", "sha256": "0wiaczf6qvi5qaidjp7hlfh5d054dswalgwrf9a4xd6407nx6nj5", "depends": ["Biobase", "httr", "jsonlite", "limma", "oligo", "rlang"] }, "AssessORF": { "name": "AssessORF", "version": "1.26.0", "sha256": "1wd1xr2f25l418klvr7dwjvv9n8x51qg4la3i354q5vrjj0y5hrp", "depends": ["Biostrings", "DECIPHER", "GenomicRanges", "IRanges"] }, "BADER": { "name": "BADER", "version": "1.46.0", "sha256": "00ma4zx6nha1x0iwcpzq0a4ajw2gm9k5zvq5n6ambdy5cf22z0nx", "depends": [] }, "BAGS": { "name": "BAGS", "version": "2.48.0", "sha256": "1s0fqs4chr8ixxlq3a5scnncrq3bma6vz1s1isdwwxf57vp6d1v2", "depends": ["Biobase", "breastCancerVDX"] }, "BANDITS": { "name": "BANDITS", "version": "1.24.0", "sha256": "1xqi3gpsshnb6h1yyvxh4dqafzw691zmpy4mc40nd6skz3hqwls0", "depends": ["BiocParallel", "DRIMSeq", "MASS", "R_utils", "Rcpp", "RcppArmadillo", "data_table", "doParallel", "doRNG", "foreach", "ggplot2"] }, "BASiCS": { "name": "BASiCS", "version": "2.20.0", "sha256": "0wlsamynz8230h4yp8vqdmdh5n8ky1bnp6dr906cswfj89zn4yiv", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "MASS", "Matrix", "Rcpp", "RcppArmadillo", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "assertthat", "coda", "cowplot", "ggExtra", "ggplot2", "hexbin", "matrixStats", "posterior", "reshape2", "scran", "scuttle", "viridis"] }, "BASiCStan": { "name": "BASiCStan", "version": "1.10.0", "sha256": "0i4m777lfy5v8j6mzh3sj0g411q1n89kdf8hqaaznblx73r1af9f", "depends": ["BASiCS", "BH", "Rcpp", "RcppEigen", "RcppParallel", "SingleCellExperiment", "StanHeaders", "SummarizedExperiment", "glmGamPoi", "rstan", "rstantools", "scran", "scuttle"] }, "BBCAnalyzer": { "name": "BBCAnalyzer", "version": "1.38.0", "sha256": "1qs25p1cj7k8j88w193c35fidgz3hfprsd8bsrk9nfvsg399g0py", "depends": ["Biostrings", "GenomicRanges", "IRanges", "Rsamtools", "SummarizedExperiment", "VariantAnnotation"] }, "BCRANK": { "name": "BCRANK", "version": "1.70.0", "sha256": "0jgryr10fyivrj5yhqdnikbkif2g53v4mhyfczb9z0c7p1vipcc6", "depends": ["Biostrings"] }, "BEAT": { "name": "BEAT", "version": "1.46.0", "sha256": "0fd1yd1pl4zvxnmq10w6fl6a0xzgghhl4by00dxiiqrwfsqnh7sv", "depends": ["BSgenome", "Biostrings", "GenomicRanges", "ShortRead"] }, "BERT": { "name": "BERT", "version": "1.4.0", "sha256": "1y1knq38fp3frw7c1j45xps1pvqfa5909hdj5v5n58vzxb4qxnnq", "depends": ["BiocParallel", "SummarizedExperiment", "cluster", "comprehenr", "foreach", "invgamma", "iterators", "janitor", "limma", "logging", "sva"] }, "BEclear": { "name": "BEclear", "version": "2.24.0", "sha256": "158ca135lsxjj523gv31cqdc6321fpyjvc652dpyfbva0xbz7qw7", "depends": ["BiocParallel", "Matrix", "Rcpp", "Rdpack", "abind", "data_table", "dixonTest", "futile_logger", "ids"] }, "BG2": { "name": "BG2", "version": "1.8.0", "sha256": "0d6ck2x60nw5zqplalgvqm2093lqirin1lp91ihdj1hmhfbpy1zz", "depends": ["GA", "MASS", "Matrix", "caret", "memoise"] }, "BLMA": { "name": "BLMA", "version": "1.32.0", "sha256": "1lqfim34rci17hl27hi3cmp40wikfxq5vkjvqrrzh9cs7nvi0kns", "depends": ["Biobase", "GSA", "PADOG", "ROntoTools", "graph", "limma", "metafor"] }, "BOBaFIT": { "name": "BOBaFIT", "version": "1.12.0", "sha256": "0pfkdcsl6bwvaad0dwina5k7ajchpknkfp6v6ircic5yxvi6yd25", "depends": ["GenomicRanges", "NbClust", "dplyr", "ggbio", "ggforce", "ggplot2", "magrittr", "plyranges", "stringr", "tidyr"] }, "BPRMeth": { "name": "BPRMeth", "version": "1.34.0", "sha256": "0p06wjxmhfq3nyz1cwj0ghl3rnwd9lkhgzrndzgxb2a9l6v74w2h", "depends": ["BiocStyle", "GenomicRanges", "IRanges", "MASS", "Rcpp", "RcppArmadillo", "S4Vectors", "assertthat", "cowplot", "data_table", "doParallel", "e1071", "earth", "foreach", "ggplot2", "kernlab", "magrittr", "matrixcalc", "mvtnorm", "randomForest", "truncnorm"] }, "BRAIN": { "name": "BRAIN", "version": "1.54.0", "sha256": "11zd5z9xd9564cqh6lzl3wgi15170w4cbi0np18v2fmc3hkm2gzh", "depends": ["Biostrings", "PolynomF", "lattice"] }, "BREW3R_r": { "name": "BREW3R.r", "version": "1.4.0", "sha256": "0m8ivr5wx7z7ymwzk5kjhczrhr81i92lf2ph6qz58yg1xzqvmxmi", "depends": ["GenomicRanges", "S4Vectors", "rlang"] }, "BSgenome": { "name": "BSgenome", "version": "1.76.0", "sha256": "0xlfznvccvk6ymnk41bsdif4pgkh90xpsq9c67rsjrza71cl31f0", "depends": ["BiocGenerics", "BiocIO", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "XVector", "matrixStats", "rtracklayer"] }, "BSgenomeForge": { "name": "BSgenomeForge", "version": "1.8.0", "sha256": "0118mxyg8xxkwkfg6k1zw2xnx4b6zacf3bn9jy0kfks555cfbjsy", "depends": ["BSgenome", "Biobase", "BiocGenerics", "BiocIO", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "rtracklayer"] }, "BUMHMM": { "name": "BUMHMM", "version": "1.32.0", "sha256": "0anmnwbpcrz0n5zwf80cb4zxmybhxf94ayzyxpilfb04xg1j77dm", "depends": ["Biostrings", "IRanges", "SummarizedExperiment", "devtools", "gtools", "stringi"] }, "BUS": { "name": "BUS", "version": "1.64.0", "sha256": "1x017881b1zw3hnfj45llmrkn76qrzqirfyv1ldif7lkg2a00qkz", "depends": ["infotheo", "minet"] }, "BUScorrect": { "name": "BUScorrect", "version": "1.26.0", "sha256": "13l3x9jdfcdh8aswvqkhk1gjbz8y6nl3v4lbhw57w1smxlj9gz3g", "depends": ["SummarizedExperiment", "gplots"] }, "BUSpaRse": { "name": "BUSpaRse", "version": "1.22.1", "sha256": "1rlzw7p8mzfw20a9njnaam2y5895ccakhvzkw70p5zsx3vf76vzv", "depends": ["AnnotationDbi", "AnnotationFilter", "BH", "BSgenome", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "Rcpp", "RcppArmadillo", "RcppProgress", "S4Vectors", "biomaRt", "dplyr", "ensembldb", "ggplot2", "magrittr", "plyranges", "stringr", "tibble", "tidyr", "zeallot"] }, "BUSseq": { "name": "BUSseq", "version": "1.14.0", "sha256": "0sxjwrh3vcpi5sf80mkcnx3jsl53xla9qrhpq6mxfg61gx9psdwh", "depends": ["S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "gplots"] }, "BaalChIP": { "name": "BaalChIP", "version": "1.34.0", "sha256": "05l8n7yff1gkfcbv6d4j4sa4fyx8d99j87k0hdi9mi903l0kwidi", "depends": ["GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "coda", "doBy", "doParallel", "foreach", "ggplot2", "reshape2", "scales"] }, "BadRegionFinder": { "name": "BadRegionFinder", "version": "1.36.0", "sha256": "1b6chw8h8vv38gifnn51zmdbgqkfkamq761hvmsqm8vhbfm6sgm9", "depends": ["GenomicRanges", "Rsamtools", "S4Vectors", "VariantAnnotation", "biomaRt"] }, "Banksy": { "name": "Banksy", "version": "1.4.0", "sha256": "0s01d9wli074970qpbb235vpb2s1ni0b4ay6gl4blcp4g5q3327c", "depends": ["RcppHungarian", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "aricode", "data_table", "dbscan", "igraph", "irlba", "leidenAlg", "matrixStats", "mclust", "uwot"] }, "BaseSpaceR": { "name": "BaseSpaceR", "version": "1.52.0", "sha256": "10h6wq1b8lyh7dnxxwsjxy06y32r16k0r4knaj6zrij9d1in6yw0", "depends": ["RCurl", "RJSONIO"] }, "Basic4Cseq": { "name": "Basic4Cseq", "version": "1.44.0", "sha256": "1b27061iznhajcdis6r86cwid4y35m8j6si7h0winw1j87rhdg14", "depends": ["BSgenome_Ecoli_NCBI_20080805", "Biostrings", "GenomicAlignments", "GenomicRanges", "RCircos", "caTools"] }, "BasicSTARRseq": { "name": "BasicSTARRseq", "version": "1.36.0", "sha256": "195cpbmnz2hl1yxjq86qjdk2ns96bhvjq89kv379pq8xiais3mmz", "depends": ["GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "S4Vectors"] }, "BatchQC": { "name": "BatchQC", "version": "2.4.0", "sha256": "1bqi8ypwdz6mlk6k4h8spw49qmq70ln8s6jx6rdizgv136b8q3ls", "depends": ["DESeq2", "EBSeq", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "data_table", "dplyr", "ggdendro", "ggnewscale", "ggplot2", "limma", "matrixStats", "pheatmap", "reader", "reshape2", "scran", "shiny", "shinyjs", "shinythemes", "sva", "tibble", "tidyr", "tidyverse", "umap"] }, "BatchSVG": { "name": "BatchSVG", "version": "1.0.0", "sha256": "1bwvziwl8wxkn26fiz76sr06w3j2ldwin88s49iqaq27wlr19b75", "depends": ["RColorBrewer", "SummarizedExperiment", "cowplot", "dplyr", "ggplot2", "ggrepel", "rlang", "scales", "scry"] }, "BayesKnockdown": { "name": "BayesKnockdown", "version": "1.34.0", "sha256": "18jmsgdyvg5m3kndzcszjgfwfh0bwmi3nvfyg4nl9l0skp478cld", "depends": ["Biobase"] }, "BayesSpace": { "name": "BayesSpace", "version": "1.18.4", "sha256": "11d05flnpc284k5mbymsc5l4ij81g1v3nxf92slmakwkwwm689gn", "depends": ["BiocFileCache", "BiocParallel", "BiocSingular", "DirichletReg", "Matrix", "RCurl", "Rcpp", "RcppArmadillo", "RcppDist", "RcppProgress", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "arrow", "assertthat", "coda", "dplyr", "ggplot2", "magrittr", "mclust", "microbenchmark", "purrr", "rhdf5", "rjson", "rlang", "scales", "scater", "scran", "tibble", "tidyr", "xgboost"] }, "BeadDataPackR": { "name": "BeadDataPackR", "version": "1.60.0", "sha256": "066cjf2ir95xzc97a7ir2lhnpgzzhdgylv6ly0xvybjfbimq99a7", "depends": [] }, "BgeeCall": { "name": "BgeeCall", "version": "1.24.1", "sha256": "0xkrl2c31hkqb6px59274sxnr10apdyyi4yl040di0rl40f23qsr", "depends": ["AnnotationDbi", "Biostrings", "GenomicFeatures", "IRanges", "RCurl", "RSQLite", "curl", "data_table", "dplyr", "ggplot2", "jsonlite", "readr", "rhdf5", "rslurm", "rtracklayer", "scales", "sjmisc", "spatstat_univar", "stringr", "txdbmaker", "tximport"] }, "BgeeDB": { "name": "BgeeDB", "version": "2.34.0", "sha256": "0haf6khbm695dyi2f6npm7yx2gbz29kvi62qln1h1nj0k3qw0afi", "depends": ["Biobase", "HDF5Array", "RCurl", "RSQLite", "R_utils", "anndata", "bread", "curl", "data_table", "digest", "dplyr", "graph", "tidyr", "topGO", "zellkonverter"] }, "BiFET": { "name": "BiFET", "version": "1.28.0", "sha256": "0qc715kqiky0r9kn1hhnmqd987im9v4awg0jg7nlp3yv5isl0m90", "depends": ["GenomicRanges", "poibin"] }, "BiGGR": { "name": "BiGGR", "version": "1.44.0", "sha256": "1awdwwg54cfnsn8kp0lw6a7c3mgix024ry7mxn9vb5xq4hp1gflb", "depends": ["hyperdraw", "hypergraph", "limSolve", "rsbml", "stringr"] }, "BiRewire": { "name": "BiRewire", "version": "3.40.0", "sha256": "0amv3ralspzj1s5md7maxdr2abysnjrizlvcfjvdnb68ryv86wwa", "depends": ["Matrix", "Rtsne", "igraph", "slam"] }, "BiSeq": { "name": "BiSeq", "version": "1.48.1", "sha256": "04x2nab4mhrcrv73g5pg6gdi0fw91gn1qg0mn5xq63b9nww7zyw3", "depends": ["Biobase", "BiocGenerics", "Formula", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "betareg", "globaltest", "lokern", "rtracklayer"] }, "BicARE": { "name": "BicARE", "version": "1.66.0", "sha256": "17nbww1fnqnq5jzl54pszva6sf9ic730ph9klcsyay01z54lk7j0", "depends": ["Biobase", "GO_db", "GSEABase", "multtest"] }, "BindingSiteFinder": { "name": "BindingSiteFinder", "version": "2.6.0", "sha256": "1m3bli4jpjqcaif28pbd7d06q2q354h5adf8l3kk4m4v2dvjqh8v", "depends": ["ComplexHeatmap", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "dplyr", "forcats", "ggdist", "ggforce", "ggplot2", "kableExtra", "lifecycle", "matrixStats", "plyr", "rlang", "rtracklayer", "tibble", "tidyr"] }, "BioCartaImage": { "name": "BioCartaImage", "version": "1.6.0", "sha256": "1xzjvn39hnw5fjkm71c7lv6k2wzyxsxnkkhxwj7xhs723m8pfxxb", "depends": ["magick"] }, "BioCor": { "name": "BioCor", "version": "1.32.0", "sha256": "0kb970wqdj1csgprfr4wdiz90vk1ibqc684kpnhlja8zh0s2p92n", "depends": ["BiocParallel", "GSEABase", "Matrix"] }, "BioGA": { "name": "BioGA", "version": "1.2.0", "sha256": "18ralrpz8cfk6ab5hmz4zn3nz6dcvl8kkhiqj30qw8pk6c2pdkjn", "depends": ["BiocStyle", "Rcpp", "SummarizedExperiment", "animation", "biocViews", "ggplot2", "rlang", "sessioninfo"] }, "BioMVCClass": { "name": "BioMVCClass", "version": "1.76.0", "sha256": "03w97bix5xlb6v06ffmlj1nbyl11j6qrb1a54m7wdrvranmr7msl", "depends": ["Biobase", "MVCClass", "Rgraphviz", "graph"] }, "BioNAR": { "name": "BioNAR", "version": "1.10.0", "sha256": "0l675wbsvjh0p91fs17p47ldhmlllkvvdp8n84ch2j1mfqmxz39n", "depends": ["AnnotationDbi", "GO_db", "Matrix", "RSpectra", "Rdpack", "WGCNA", "cowplot", "data_table", "dplyr", "fgsea", "ggplot2", "ggrepel", "igraph", "latex2exp", "minpack_lm", "org_Hs_eg_db", "poweRlaw", "rSpectral", "scales", "stringr", "viridis"] }, "BioNERO": { "name": "BioNERO", "version": "1.16.0", "sha256": "1cih9d9a0ncn65gylw6bi49n25s8v6scglsmka0fv9fncypaqc7h", "depends": ["BiocParallel", "ComplexHeatmap", "GENIE3", "NetRep", "RColorBrewer", "SummarizedExperiment", "WGCNA", "dynamicTreeCut", "ggdendro", "ggnetwork", "ggplot2", "ggrepel", "igraph", "intergraph", "matrixStats", "minet", "patchwork", "reshape2", "rlang", "sva"] }, "BioNet": { "name": "BioNet", "version": "1.68.0", "sha256": "0a0pd7bhmgxa8yl9qfk4ns1vbvfxvclb2gblslfwmp7blqayhva3", "depends": ["AnnotationDbi", "Biobase", "RBGL", "graph", "igraph"] }, "BioQC": { "name": "BioQC", "version": "1.36.0", "sha256": "0waw9hkf879hmyb2s1bhnia0sygr4z46815frbxdir5q9m6w7zhc", "depends": ["Biobase", "Rcpp", "edgeR"] }, "BioTIP": { "name": "BioTIP", "version": "1.22.0", "sha256": "0xrsni2gnzis5ids5c2xlm2qzhplr9ny54jc65a798r072v1yilc", "depends": ["GenomicRanges", "MASS", "cluster", "igraph", "psych", "scran", "stringr"] }, "Biobase": { "name": "Biobase", "version": "2.68.0", "sha256": "03vzsm6m8wbmrg997k3qczr6jfwin9qxfxmq3lal6l1yk9vk0fwr", "depends": ["BiocGenerics"] }, "BiocBaseUtils": { "name": "BiocBaseUtils", "version": "1.10.0", "sha256": "1ssva33zg6n6j8k6v3cnl6nrllm371jp7l20wh00mj70garaizkw", "depends": [] }, "BiocBook": { "name": "BiocBook", "version": "1.6.0", "sha256": "1kc4n2mrny4zmdg2lhf4b9gcnhmx34wn8h55ladnkkx2llgjb89v", "depends": ["BiocGenerics", "available", "cli", "dplyr", "gert", "gh", "gitcreds", "glue", "httr", "purrr", "quarto", "renv", "rlang", "rprojroot", "stringr", "tibble", "usethis", "yaml"] }, "BiocCheck": { "name": "BiocCheck", "version": "1.44.2", "sha256": "0i8ndbz3jjgr8p6z4lhk4c27w3f9psnbpxw678zw1cg3c7k33qln", "depends": ["BiocBaseUtils", "BiocFileCache", "BiocManager", "biocViews", "callr", "cli", "codetools", "graph", "httr2", "knitr", "rvest", "stringdist"] }, "BiocFHIR": { "name": "BiocFHIR", "version": "1.10.0", "sha256": "0569szdaz94k2vaz1jjwybnc49i8izdvx0agzh38356xjsv05d79", "depends": ["BiocBaseUtils", "DT", "dplyr", "graph", "jsonlite", "shiny", "tidyr", "visNetwork"] }, "BiocFileCache": { "name": "BiocFileCache", "version": "2.16.1", "sha256": "0plnrd95jxkmiy624a7wdvsb73k2sn75b2z2ylvrd8whzzk39b1y", "depends": ["DBI", "RSQLite", "curl", "dbplyr", "dplyr", "filelock", "httr"] }, "BiocGenerics": { "name": "BiocGenerics", "version": "0.54.0", "sha256": "1fa11kh0d4sxjac22p2kjxj5v0dg32vldz7fcdzi8wf6rds6yga1", "depends": ["generics"] }, "BiocHail": { "name": "BiocHail", "version": "1.7.1", "sha256": "1ik7yqjvwk3nyqsq39y888d0fd1rbrnlana6sj2r73xppm8ic3iw", "depends": ["BiocFileCache", "BiocGenerics", "basilisk", "dplyr", "reticulate"] }, "BiocHubsShiny": { "name": "BiocHubsShiny", "version": "1.8.1", "sha256": "12ihq8c0byrf6xiqbbmlzv79sq4xy7sjw06v3apn08gvypl0ifys", "depends": ["AnnotationHub", "DT", "ExperimentHub", "S4Vectors", "htmlwidgets", "rclipboard", "shiny", "shinyAce", "shinyjs", "shinythemes", "shinytoastr"] }, "BiocIO": { "name": "BiocIO", "version": "1.18.0", "sha256": "0sjvxzw110qrigfnhzmbzi16nhvfhqa7lj1yly5r4pqkpj77sdrs", "depends": ["BiocGenerics", "S4Vectors"] }, "BiocNeighbors": { "name": "BiocNeighbors", "version": "2.2.0", "sha256": "01fnlbh57y989cdcki5zpbva7q7fj5sw9vrx3pjh51riqy8nnniw", "depends": ["Rcpp", "assorthead"] }, "BiocParallel": { "name": "BiocParallel", "version": "1.42.1", "sha256": "0dandzqfalf3d1w99yajiahrg4c1xjr8gmw11bhaacr6rvgbbdxg", "depends": ["BH", "codetools", "cpp11", "futile_logger", "snow"] }, "BiocPkgTools": { "name": "BiocPkgTools", "version": "1.26.2", "sha256": "1zk3sw5vwgx1rl16s52cs8a3zmn1x95wsda1djiw8l4g45vnbjyz", "depends": ["BiocFileCache", "BiocManager", "DT", "RBGL", "biocViews", "curl", "dplyr", "gh", "glue", "graph", "htmltools", "htmlwidgets", "httr", "igraph", "jsonlite", "lubridate", "purrr", "readr", "rlang", "rorcid", "rvest", "stringr", "tibble", "tidyr", "xml2", "yaml"] }, "BiocSet": { "name": "BiocSet", "version": "1.22.0", "sha256": "1lnk8j22v75vr5wq501976i2ny43jqd3ixwk4yfrb531acvz2yd7", "depends": ["AnnotationDbi", "BiocIO", "KEGGREST", "S4Vectors", "dplyr", "ontologyIndex", "plyr", "rlang", "tibble", "tidyr"] }, "BiocSingular": { "name": "BiocSingular", "version": "1.24.0", "sha256": "0dmlx6jshwh1iwmwjz9p8iykv34jskl9z6kxdxcbrl38wzsjhjfy", "depends": ["BiocGenerics", "BiocParallel", "DelayedArray", "Matrix", "Rcpp", "S4Vectors", "ScaledMatrix", "assorthead", "beachmat", "irlba", "rsvd"] }, "BiocSklearn": { "name": "BiocSklearn", "version": "1.30.0", "sha256": "15fyjg2pf77cnqzbb5hcbg3wc9kqn6hnklivhb3797v1za9y283x", "depends": ["SummarizedExperiment", "basilisk", "reticulate"] }, "BiocStyle": { "name": "BiocStyle", "version": "2.36.0", "sha256": "1q186nrib86gicgv54h3snyah8kq8vc1vrzn81l5ly1hkgrn7fnl", "depends": ["BiocManager", "bookdown", "knitr", "rmarkdown", "yaml"] }, "BiocVersion": { "name": "BiocVersion", "version": "3.21.1", "sha256": "1xvfcvlg8984mfb99nml8p8liyb7w6myznhp2kvr8cy8x7g60p4q", "depends": [] }, "BiocWorkflowTools": { "name": "BiocWorkflowTools", "version": "1.34.0", "sha256": "07g8snhhjwl7vcsm2k9kim8b167awr94axalr0hzq81w5k6ajs1d", "depends": ["BiocStyle", "bookdown", "git2r", "httr", "knitr", "rmarkdown", "rstudioapi", "stringr", "usethis"] }, "Biostrings": { "name": "Biostrings", "version": "2.76.0", "sha256": "1fwkpqf3m6hq305fiw371hmkldwvbcgdbhsc3vf477xighyhqh85", "depends": ["BiocGenerics", "GenomeInfoDb", "IRanges", "S4Vectors", "XVector", "crayon"] }, "BloodGen3Module": { "name": "BloodGen3Module", "version": "1.16.0", "sha256": "011k9jl84gg5m9j1qg818wq3bixzy1hqzlz8an3h6w9rm3gcsfwb", "depends": ["ComplexHeatmap", "ExperimentHub", "SummarizedExperiment", "V8", "circlize", "ggplot2", "gtools", "limma", "matrixStats", "preprocessCore", "randomcoloR", "reshape2", "testthat"] }, "BreastSubtypeR": { "name": "BreastSubtypeR", "version": "1.0.0", "sha256": "1r5fmks5x4al3wldmy5lspcbpiwvp93glfc1r95arx011462kx92", "depends": ["Biobase", "ComplexHeatmap", "RColorBrewer", "SummarizedExperiment", "circlize", "data_table", "dplyr", "e1071", "ggplot2", "ggrepel", "impute", "magrittr", "rlang", "stringr", "tidyselect", "withr"] }, "BridgeDbR": { "name": "BridgeDbR", "version": "2.18.0", "sha256": "08p4d1z65pkqk78zp6sg9zimzbqzr91xci9crr4mkn3nh7ncnyhh", "depends": ["curl", "rJava"] }, "BrowserViz": { "name": "BrowserViz", "version": "2.30.0", "sha256": "18cqkq9yc9n0wiiihrr2lggp3s848x391yxb1m5gfkwk0cpyzv6h", "depends": ["BiocGenerics", "httpuv", "jsonlite"] }, "BubbleTree": { "name": "BubbleTree", "version": "2.38.0", "sha256": "1h3wyp9f554zlf4ah6dqgb1c26bkx1ks2q709hz3krchgzv3pinn", "depends": ["Biobase", "BiocGenerics", "BiocStyle", "GenomicRanges", "IRanges", "RColorBrewer", "WriteXLS", "biovizBase", "dplyr", "e1071", "ggplot2", "gridExtra", "gtable", "gtools", "limma", "magrittr", "plyr"] }, "BufferedMatrix": { "name": "BufferedMatrix", "version": "1.72.0", "sha256": "1186mmiw7pca05llgzq3lqycr0kcyb94fbrjyvvxaa7cjlzhrlni", "depends": [] }, "BufferedMatrixMethods": { "name": "BufferedMatrixMethods", "version": "1.72.0", "sha256": "0inxq1ahx57y5g2kd1spp64v4rqja8y8zich3rj8887nw6j47jiw", "depends": ["BufferedMatrix"] }, "BulkSignalR": { "name": "BulkSignalR", "version": "1.0.2", "sha256": "0dhnx48ff0kspy6dbi6cpr5wc8pwx23r3bbai6pjrfcmh54qnpz0", "depends": ["BiocFileCache", "ComplexHeatmap", "DBI", "RANN", "RCurl", "RSQLite", "Rtsne", "SpatialExperiment", "SummarizedExperiment", "circlize", "cli", "curl", "doParallel", "dplyr", "foreach", "ggalluvial", "ggplot2", "ggrepel", "glmnet", "gridExtra", "httr", "igraph", "jsonlite", "matrixStats", "multtest", "orthogene", "rlang", "scales", "stabledist"] }, "BumpyMatrix": { "name": "BumpyMatrix", "version": "1.16.0", "sha256": "1frai0sf94igvd078pnkdvhwmrwihpdqvc0rcxislpjjjl697jhp", "depends": ["IRanges", "Matrix", "S4Vectors"] }, "CAEN": { "name": "CAEN", "version": "1.16.0", "sha256": "1s7gmcnc3d9xzx8zhfqpch6brz84g4b8j2wjl27bs60bx6fwpbwa", "depends": ["PoiClaClu", "SummarizedExperiment"] }, "CAFE": { "name": "CAFE", "version": "1.44.0", "sha256": "049idq4iz68rvrdajwwcf6g2fl3wh4bwrnaflap9pivdwkm14i8s", "depends": ["Biobase", "GenomicRanges", "IRanges", "affy", "annotate", "biovizBase", "ggbio", "ggplot2", "gridExtra"] }, "CAGEfightR": { "name": "CAGEfightR", "version": "1.28.0", "sha256": "1rdnr780lbh61zyd976w64zyzvxyqz720dq80d9d2d39axym8jb9", "depends": ["BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicFiles", "GenomicInteractions", "GenomicRanges", "Gviz", "IRanges", "InteractionSet", "Matrix", "S4Vectors", "SummarizedExperiment", "assertthat", "pryr", "rtracklayer"] }, "CAGEr": { "name": "CAGEr", "version": "2.14.0", "sha256": "05aaw9lcdabn4zgi2f10s9inw1b9inwxcg05d4mj5d5jwrhs9ysc", "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "CAGEfightR", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "KernSmooth", "MultiAssayExperiment", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VGAM", "data_table", "formula_tools", "ggplot2", "gtools", "memoise", "plyr", "reshape2", "rlang", "rtracklayer", "scales", "som", "stringdist", "stringi", "vegan"] }, "CAMERA": { "name": "CAMERA", "version": "1.64.0", "sha256": "08483nkygysgvnn9acdwgibj2b8l0lrxzlwabm3jr091rhnzpazp", "depends": ["Biobase", "Hmisc", "RBGL", "graph", "igraph", "xcms"] }, "CARDspa": { "name": "CARDspa", "version": "1.0.0", "sha256": "1gsdlf6asxli78yx50pxj4yg8s2rd5msi3vq9b3brqm0bakaid6n", "depends": ["BiocParallel", "MCMCpack", "Matrix", "NMF", "RANN", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppML", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "concaveman", "dplyr", "fields", "ggcorrplot", "ggplot2", "gtools", "nnls", "reshape2", "scatterpie", "sf", "sp", "spatstat_random", "wrMisc"] }, "CARNIVAL": { "name": "CARNIVAL", "version": "2.18.0", "sha256": "1f4b8459lc8qirzdw2pn1jszipklif12wscpc9ll99pgmb65h37f", "depends": ["dplyr", "igraph", "lpSolve", "readr", "rjson", "rmarkdown", "stringr", "tibble", "tidyr"] }, "CATALYST": { "name": "CATALYST", "version": "1.32.0", "sha256": "17m2446z61mxxfcalimq47z3phla0z1zs11rkbpsc3zq8590pj83", "depends": ["ComplexHeatmap", "ConsensusClusterPlus", "FlowSOM", "Matrix", "RColorBrewer", "Rtsne", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "circlize", "cowplot", "data_table", "dplyr", "drc", "flowCore", "ggplot2", "ggrepel", "ggridges", "gridExtra", "matrixStats", "nnls", "purrr", "reshape2", "scales", "scater"] }, "CBNplot": { "name": "CBNplot", "version": "1.8.0", "sha256": "13w72kjdyrk6zmb9aq0y63q166smndhvzyx0cwgcbfpl3nz18w3r", "depends": ["BiocFileCache", "ExperimentHub", "Rmpfr", "bnlearn", "clusterProfiler", "depmap", "dplyr", "enrichplot", "ggdist", "ggforce", "ggplot2", "ggraph", "graphite", "graphlayouts", "igraph", "magrittr", "org_Hs_eg_db", "patchwork", "purrr", "pvclust", "reshape2", "rlang", "stringr", "tidyr"] }, "CCAFE": { "name": "CCAFE", "version": "1.0.0", "sha256": "11j26rgg87wdcg6figpdg0s4944s575drz1k17wwgc9xa6vg6wv1", "depends": ["VariantAnnotation", "dplyr"] }, "CCPROMISE": { "name": "CCPROMISE", "version": "1.34.0", "sha256": "1wbcpksxw917jggm15z6bzbgrkqavb6rd64j7yj3wr3fhbyq3b0b", "depends": ["Biobase", "CCP", "GSEABase", "PROMISE"] }, "CCPlotR": { "name": "CCPlotR", "version": "1.6.0", "sha256": "1jbfqffavawp48ljc6pnfn5n68yrasp68jwr8v8gf4d7bcig590q", "depends": ["ComplexHeatmap", "RColorBrewer", "circlize", "dplyr", "forcats", "ggbump", "ggh4x", "ggplot2", "ggraph", "ggtext", "igraph", "patchwork", "plyr", "scales", "scatterpie", "stringr", "tibble", "tidyr", "viridis"] }, "CDI": { "name": "CDI", "version": "1.6.0", "sha256": "1lr5h0wh4ib7nzbcfsgn51iwz31rqfljk5wk937hvgh2p0in19gg", "depends": ["BiocParallel", "Seurat", "SeuratObject", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "ggsci", "matrixStats", "reshape2"] }, "CEMiTool": { "name": "CEMiTool", "version": "1.32.0", "sha256": "1havqmgai0vdm0w1mwajflkqn8hilrsa4hgchwbq13rfhrb5ykjm", "depends": ["DT", "WGCNA", "clusterProfiler", "data_table", "dplyr", "fastcluster", "fgsea", "ggdendro", "ggplot2", "ggpmisc", "ggrepel", "ggthemes", "gridExtra", "gtable", "htmltools", "igraph", "intergraph", "knitr", "matrixStats", "network", "pracma", "rmarkdown", "scales", "sna", "stringr"] }, "CFAssay": { "name": "CFAssay", "version": "1.42.0", "sha256": "0qbn86fhv35kqxnnb5g1nkd3767r2f5j9fqbqgw3h660q84qxi02", "depends": [] }, "CGEN": { "name": "CGEN", "version": "3.44.0", "sha256": "03iysky09hfm348350mhx199frdr766b1ln4ppp1ja5qx3gw8r78", "depends": ["mvtnorm", "survival"] }, "CGHbase": { "name": "CGHbase", "version": "1.68.0", "sha256": "1kp2isq47x6z0wysx0jbxqjr4zsr118bw9jx4r2k6jqf6ikpsbdj", "depends": ["Biobase", "marray"] }, "CGHcall": { "name": "CGHcall", "version": "2.70.0", "sha256": "1ygfzla36h3bgj9j480xlgczn473r894d0yy10wvfi01rcpgmccn", "depends": ["Biobase", "CGHbase", "DNAcopy", "impute", "snowfall"] }, "CGHnormaliter": { "name": "CGHnormaliter", "version": "1.62.0", "sha256": "0d1g24xglli0zgkysk95827rwylpv0w0sz2zhh7cnzqcbdyplwch", "depends": ["Biobase", "CGHbase", "CGHcall"] }, "CGHregions": { "name": "CGHregions", "version": "1.66.0", "sha256": "016g4wzb4c3wacpp7f684l0ncqb70s7w29fcvxk4vgr9b6mh70id", "depends": ["Biobase", "CGHbase"] }, "CHETAH": { "name": "CHETAH", "version": "1.24.0", "sha256": "1zwxkzfqgdc3qyb2pxr5z7azly1z91pcl0zlfk2qlxdi9p6a0xbj", "depends": ["S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "bioDist", "corrplot", "cowplot", "dendextend", "ggplot2", "pheatmap", "plotly", "reshape2", "shiny"] }, "CHRONOS": { "name": "CHRONOS", "version": "1.36.0", "sha256": "1lvski7p05zv8zziimhfacpq8y3nay6awngm1dgs8r494a8k0kax", "depends": ["RBGL", "RCurl", "XML", "biomaRt", "circlize", "doParallel", "foreach", "graph", "igraph", "openxlsx", "rJava"] }, "CIMICE": { "name": "CIMICE", "version": "1.16.0", "sha256": "1xvbrqs5m19dhnqkpadqqcxjizc6g55v66lbqljqi1l1rzqhsq00", "depends": ["Matrix", "assertthat", "dplyr", "expm", "ggcorrplot", "ggplot2", "ggraph", "glue", "igraph", "maftools", "networkD3", "purrr", "tidygraph", "tidyr", "visNetwork"] }, "CINdex": { "name": "CINdex", "version": "1.36.0", "sha256": "1cdmmnyxsrzlnsp15i8b072dfdsglql89ss1ddcwh4jyg8svwakl", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "bitops", "dplyr", "gplots", "gridExtra", "png", "som", "stringr"] }, "CMA": { "name": "CMA", "version": "1.66.0", "sha256": "152g2w3nvva6z637j3l1g1v0kpfs2pqzcdkhphkbahjii9svxl8s", "depends": ["Biobase"] }, "CNAnorm": { "name": "CNAnorm", "version": "1.54.0", "sha256": "1c54y6cswl6vfk222p22qszqina3m4ppc7m2g9a3d82ipi7gcxl4", "depends": ["DNAcopy"] }, "CNEr": { "name": "CNEr", "version": "1.43.0", "sha256": "129092mvpfiglf63z00himz39m5xw4dizrq70zg1l4s357cbbi9h", "depends": ["BiocGenerics", "Biostrings", "DBI", "GO_db", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "KEGGREST", "RSQLite", "R_utils", "S4Vectors", "XVector", "annotate", "ggplot2", "poweRlaw", "pwalign", "readr", "reshape2", "rtracklayer"] }, "CNORdt": { "name": "CNORdt", "version": "1.50.0", "sha256": "01dcgbyb656yw23ihnsbwwid1zz11s9f75zh5fp0w5lg1bmxpmmv", "depends": ["CellNOptR", "abind"] }, "CNORfeeder": { "name": "CNORfeeder", "version": "1.48.0", "sha256": "0lihig0j3x4nf5y1m8f12d1iwd5v6svh7754j71111il85kdgjcs", "depends": ["CellNOptR", "graph"] }, "CNORfuzzy": { "name": "CNORfuzzy", "version": "1.50.0", "sha256": "1zxvl98k2w308l29h16h2gn16r880n7nqw5z9rx8fsncv1g6k4s8", "depends": ["CellNOptR", "nloptr"] }, "CNORode": { "name": "CNORode", "version": "1.50.0", "sha256": "0ax75f1xsnxgnxpvlwiw1idng7l6dcx25jqgsv9i2jpjzhvypm97", "depends": ["CellNOptR", "genalg"] }, "CNTools": { "name": "CNTools", "version": "1.64.0", "sha256": "0pysvvk826aj9x017jbma92p55w52sb57imsx5pzdiqvjx4ip47x", "depends": ["genefilter"] }, "CNVMetrics": { "name": "CNVMetrics", "version": "1.12.0", "sha256": "16h04vba4x8xwisghgnmwy95hy24hgbhhrlpq1ncxgglr7vrgq58", "depends": ["BiocParallel", "GenomicRanges", "IRanges", "S4Vectors", "gridExtra", "magrittr", "pheatmap", "rBeta2009"] }, "CNVPanelizer": { "name": "CNVPanelizer", "version": "1.40.0", "sha256": "0b5iil4pivcr5j1xfv5ix9p570f6m1aalibrzcj81s2a044rk4rv", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "NOISeq", "Rsamtools", "S4Vectors", "foreach", "ggplot2", "gplots", "openxlsx", "plyr", "reshape2", "shiny", "shinyFiles", "shinyjs", "stringr", "testthat"] }, "CNVRanger": { "name": "CNVRanger", "version": "1.24.2", "sha256": "1lvsd4gif8npxz9h5pvl4r8b2by3xnngk43cg052h9vlijn499xw", "depends": ["BiocGenerics", "BiocParallel", "GDSArray", "GenomeInfoDb", "GenomicRanges", "IRanges", "RaggedExperiment", "S4Vectors", "SNPRelate", "SummarizedExperiment", "data_table", "edgeR", "gdsfmt", "lattice", "limma", "plyr", "qqman", "rappdirs", "reshape2"] }, "CNVfilteR": { "name": "CNVfilteR", "version": "1.22.0", "sha256": "1bfv1mrxa4jvzg6q8circwvdlllsc8pg5a9lq69p3l0wid10c8d5", "depends": ["Biostrings", "CopyNumberPlots", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "SummarizedExperiment", "VariantAnnotation", "assertthat", "karyoploteR", "pracma", "regioneR"] }, "CNViz": { "name": "CNViz", "version": "1.16.0", "sha256": "167a7v3r7ngfnsf7j1sblb7h2myqz9rfi17syp1v5g4w3k0p6nv7", "depends": ["CopyNumberPlots", "DT", "GenomicRanges", "dplyr", "karyoploteR", "magrittr", "plotly", "scales", "shiny"] }, "CNVrd2": { "name": "CNVrd2", "version": "1.46.0", "sha256": "05ljlfbrvy8h9piwn3vjw3b24nrqz3xmngygak3zz7v2iwrw8iy1", "depends": ["DNAcopy", "IRanges", "Rsamtools", "VariantAnnotation", "ggplot2", "gridExtra", "rjags"] }, "COCOA": { "name": "COCOA", "version": "2.22.0", "sha256": "0ppfwrv447rsb7583m22s54s9ha0iq8vvjc25xj99sgbbm2q5zs0", "depends": ["Biobase", "BiocGenerics", "ComplexHeatmap", "GenomicRanges", "IRanges", "MIRA", "S4Vectors", "data_table", "fitdistrplus", "ggplot2", "simpleCache", "tidyr"] }, "CODEX": { "name": "CODEX", "version": "1.40.0", "sha256": "0lf8rqp0m2bk93s1kg5zdz2lxipkm5lgp3y15h6bmm6f90d18caz", "depends": ["BSgenome_Hsapiens_UCSC_hg19", "Biostrings", "GenomeInfoDb", "IRanges", "Rsamtools", "S4Vectors"] }, "COMPASS": { "name": "COMPASS", "version": "1.46.0", "sha256": "09dj3m3fcqzc32i3kw4azfp4jn1v43z32vgp9n7j9jav5k7lh5ji", "depends": ["BiocStyle", "RColorBrewer", "Rcpp", "abind", "clue", "coda", "data_table", "dplyr", "foreach", "knitr", "magrittr", "pdist", "plyr", "reshape2", "rlang", "rmarkdown", "scales", "tidyr"] }, "CONFESS": { "name": "CONFESS", "version": "1.36.0", "sha256": "16szf3jgrxp391b1syjjp39q2c0hxy7f0mqaqzl6lx6bf995wigc", "depends": ["EBImage", "MASS", "SamSPECTRAL", "changepoint", "cluster", "contrast", "data_table", "ecp", "flexmix", "flowClust", "flowCore", "flowMeans", "flowMerge", "flowPeaks", "foreach", "ggplot2", "limma", "moments", "outliers", "plotrix", "raster", "readbitmap", "reshape2", "waveslim", "wavethresh", "zoo"] }, "CONSTANd": { "name": "CONSTANd", "version": "1.16.0", "sha256": "1cgis1zdsm445hmjw8bwqzqxmdb7rw0j4alxswfnnvm1vca7qba7", "depends": [] }, "COSNet": { "name": "COSNet", "version": "1.42.0", "sha256": "0b3ajdax3873x172fzvp22g6i9ckdznsw8njy74afc8kajm3aw8l", "depends": [] }, "COTAN": { "name": "COTAN", "version": "2.8.5", "sha256": "036l4ahlq8l2xyb5rabirpyy17amvflv0pw8021af4gxg3dnf1h8", "depends": ["BiocSingular", "ComplexHeatmap", "Matrix", "RColorBrewer", "Rfast", "S4Vectors", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "assertthat", "circlize", "dendextend", "dplyr", "gghalves", "ggplot2", "ggrepel", "ggthemes", "parallelDist", "parallelly", "proxy", "rlang", "scales", "stringr", "tibble", "tidyr", "withr", "zeallot"] }, "CPSM": { "name": "CPSM", "version": "1.0.0", "sha256": "0bhn6lp0z8pnjs42fcx5ybadj3c95ijx2i8bp5vsjj2jgqwmb3mz", "depends": ["Hmisc", "MASS", "MTLR", "Matrix", "ROCR", "SummarizedExperiment", "ggfortify", "ggplot2", "glmnet", "pec", "preprocessCore", "reshape2", "rms", "survival", "survivalROC", "survminer", "svglite"] }, "CRISPRball": { "name": "CRISPRball", "version": "1.4.0", "sha256": "0y1hqb6jb356qff3jclab47jkf8i65qdva3idixi20y9m009q5s8", "depends": ["ComplexHeatmap", "DT", "InteractiveComplexHeatmap", "PCAtools", "circlize", "colourpicker", "dittoSeq", "ggplot2", "htmlwidgets", "matrixStats", "plotly", "shiny", "shinyBS", "shinyWidgets", "shinycssloaders", "shinyjqui", "shinyjs"] }, "CRISPRseek": { "name": "CRISPRseek", "version": "1.48.0", "sha256": "1sr15nrf3nfrm2cvm8nkmshvlfrm9sabarymmlqf5pf7f6wq9pjh", "depends": ["BSgenome", "BiocGenerics", "Biostrings", "DelayedArray", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "XVector", "data_table", "dplyr", "gtools", "hash", "keras", "mltools", "openxlsx", "reticulate", "rhdf5", "rio", "rlang", "seqinr", "stringr"] }, "CRImage": { "name": "CRImage", "version": "1.56.0", "sha256": "0a98fhw16xy32raqi9p4h4xby3zpgbz1936lpcb2yx3g9l4mh96c", "depends": ["DNAcopy", "EBImage", "MASS", "aCGH", "e1071", "foreach", "sgeostat"] }, "CSAR": { "name": "CSAR", "version": "1.60.0", "sha256": "0qfwqayxg11zjwp0br21782a5l0a6qdyn18d4780gfpx0az34hf5", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors"] }, "CSSQ": { "name": "CSSQ", "version": "1.20.0", "sha256": "1sc5y26j34g5i3s6001dv2a0rxpiiv1f59w3xawj2n9h1ydi93pv", "depends": ["GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "SummarizedExperiment", "ggplot2", "rtracklayer"] }, "CTDquerier": { "name": "CTDquerier", "version": "2.16.0", "sha256": "1lkab41xz6md3bwma5lnmy2ypk8s01nqzwh9xap8nmn1q95rinmq", "depends": ["BiocFileCache", "RCurl", "S4Vectors", "ggplot2", "gridExtra", "igraph", "stringdist", "stringr"] }, "CTSV": { "name": "CTSV", "version": "1.10.0", "sha256": "1v2chhbk48jcq4yknc3rpk05pbhb9cci761fr4586ablvjksf7j5", "depends": ["BiocParallel", "SpatialExperiment", "SummarizedExperiment", "knitr", "pscl", "qvalue"] }, "CTdata": { "name": "CTdata", "version": "1.8.0", "sha256": "0w89npf2ygli3m7g692rjy13hi5ga07l0shf4wdbws0wk90rysvz", "depends": ["ExperimentHub"] }, "CTexploreR": { "name": "CTexploreR", "version": "1.4.0", "sha256": "0krkgl8iqz8vhvn8rcah4y1pddyjmihq3fql9wkj9s6fn2zpig4a", "depends": ["BiocGenerics", "CTdata", "ComplexHeatmap", "GenomicRanges", "IRanges", "MatrixGenerics", "SingleCellExperiment", "SummarizedExperiment", "circlize", "dplyr", "ggplot2", "ggrepel", "rlang", "tibble", "tidyr"] }, "CaDrA": { "name": "CaDrA", "version": "1.6.0", "sha256": "1kw197picmwaa03m9rx55x18pn5xdjj9xsk5f1w2lxpmq1bkrl5w", "depends": ["MASS", "R_cache", "SummarizedExperiment", "doParallel", "ggplot2", "gplots", "gtable", "knnmi", "misc3d", "plyr", "ppcor", "reshape2"] }, "CaMutQC": { "name": "CaMutQC", "version": "1.4.5", "sha256": "0zgrq0vh6klaqqlafbdihfpi7fpv7fbl130asp9xrrqgq4v7acg5", "depends": ["DT", "MesKit", "clusterProfiler", "data_table", "dplyr", "ggplot2", "maftools", "org_Hs_eg_db", "stringr", "tidyr", "vcfR"] }, "Cardinal": { "name": "Cardinal", "version": "3.10.0", "sha256": "1rik9cyw7h8gw2d8pwr0b74pj4clh9m915sj4fazfcb2d8sj6k3z", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "CardinalIO", "EBImage", "Matrix", "ProtGenerics", "S4Vectors", "irlba", "matter", "nlme"] }, "CardinalIO": { "name": "CardinalIO", "version": "1.6.0", "sha256": "067ykhkdbwiws98b8dy8prhd7v5zw23vlj2nm5j1nyhpv06p7kk9", "depends": ["BiocParallel", "S4Vectors", "matter", "ontologyIndex"] }, "Category": { "name": "Category", "version": "2.74.0", "sha256": "1faffkhi86gmnh0capmxh0gzw7vc3xy4gxnwnidz4fj3dbvcxahn", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "DBI", "GSEABase", "Matrix", "RBGL", "annotate", "genefilter", "graph"] }, "CatsCradle": { "name": "CatsCradle", "version": "1.2.0", "sha256": "16cx1blp0vh4bcf57j16wq0ny2fydmimpbhwsky8vnjzqg6wwar3", "depends": ["EBImage", "Matrix", "Rfast", "S4Vectors", "Seurat", "SeuratObject", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "abind", "data_table", "geometry", "ggplot2", "igraph", "msigdbr", "networkD3", "pheatmap", "pracma", "rdist", "reshape2", "stringr"] }, "CausalR": { "name": "CausalR", "version": "1.40.0", "sha256": "0wjc657lpi17zkb9fnp8x8mysgpp7mz5r8l5ambsqn99wnfpz0hp", "depends": ["igraph"] }, "CeTF": { "name": "CeTF", "version": "1.20.0", "sha256": "1dlrppsiw03qm7lzdfnax1zahvcmly1w5h2815jp3zp6mpnkk074", "depends": ["ComplexHeatmap", "DESeq2", "GGally", "GenomicTools_fileHandler", "Matrix", "RCy3", "Rcpp", "RcppArmadillo", "S4Vectors", "SummarizedExperiment", "circlize", "clusterProfiler", "dplyr", "ggnetwork", "ggplot2", "ggpubr", "ggrepel", "igraph", "network"] }, "CellBarcode": { "name": "CellBarcode", "version": "1.14.0", "sha256": "034p8vsxsarhyafgrqxv35c8wdm5qb2c1ddg541x4v1sba9aqjf3", "depends": ["BH", "Biostrings", "Ckmeans_1d_dp", "Rcpp", "Rsamtools", "S4Vectors", "ShortRead", "data_table", "egg", "ggplot2", "magrittr", "plyr", "seqinr", "stringr"] }, "CellBench": { "name": "CellBench", "version": "1.24.0", "sha256": "0pr1dj9c9f0gd4i7h8shwy40pzva2ncih786fs072akb83gwg7j4", "depends": ["BiocFileCache", "BiocGenerics", "BiocParallel", "SingleCellExperiment", "assertthat", "dplyr", "glue", "lubridate", "magrittr", "memoise", "purrr", "rappdirs", "rlang", "tibble", "tidyr", "tidyselect"] }, "CellMapper": { "name": "CellMapper", "version": "1.34.0", "sha256": "08fvq6qsah0a6sxgpf962027q010hvy61sjffc6s00al04awk6wf", "depends": ["S4Vectors"] }, "CellMixS": { "name": "CellMixS", "version": "1.24.0", "sha256": "053wpmv5m6m1iw5rmpsv2qm8da1r375pc65d5s2s9xcflrawdgg0", "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "SingleCellExperiment", "SummarizedExperiment", "cowplot", "dplyr", "ggplot2", "ggridges", "kSamples", "magrittr", "purrr", "scater", "tidyr", "viridis"] }, "CellNOptR": { "name": "CellNOptR", "version": "1.54.0", "sha256": "11bl03dpr4xlr5ja6a7j3zrvcmwrvr9l2jhfzkbd41v2qrxl67dw", "depends": ["RBGL", "RCurl", "Rgraphviz", "XML", "ggplot2", "graph", "igraph", "rmarkdown", "stringi", "stringr"] }, "CellScore": { "name": "CellScore", "version": "1.27.0", "sha256": "11lhb46d5w3fq8qhlmap7wfirkpdnr6bqdpdarwxirrp076znvi2", "depends": ["Biobase", "RColorBrewer", "SummarizedExperiment", "gplots", "lsa", "squash"] }, "CellTrails": { "name": "CellTrails", "version": "1.26.0", "sha256": "0y9kp9995gry4vsk0jhp8baxbdiqhs5i5qmbx1hwb660gjdb454l", "depends": ["Biobase", "BiocGenerics", "EnvStats", "Rtsne", "SingleCellExperiment", "SummarizedExperiment", "cba", "dendextend", "dtw", "ggplot2", "ggrepel", "igraph", "maptree", "mgcv", "reshape2"] }, "CelliD": { "name": "CelliD", "version": "1.16.0", "sha256": "169cvjjbzqn6q1v3m5kg1k40klwdrv7jbsmsabmqjf30xd2wjlrr", "depends": ["BiocParallel", "Matrix", "Rcpp", "RcppArmadillo", "Rtsne", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "data_table", "fastmatch", "fgsea", "ggplot2", "glue", "irlba", "matrixStats", "pbapply", "reticulate", "scater", "stringr", "tictoc", "umap"] }, "Cepo": { "name": "Cepo", "version": "1.14.0", "sha256": "0mpp3sgsrh7q65956cdlbxjrb6nfsfd67aml5qim37idakpkyhg7", "depends": ["BiocParallel", "DelayedArray", "DelayedMatrixStats", "GSEABase", "HDF5Array", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "dplyr", "ggplot2", "patchwork", "purrr", "reshape2", "rlang"] }, "CexoR": { "name": "CexoR", "version": "1.46.0", "sha256": "06hmlxiv027x6fvz4pcwkn6n2s9a4crj1q81mpdqshx0wpasky3x", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "genomation", "idr", "rtracklayer"] }, "ChAMP": { "name": "ChAMP", "version": "2.38.0", "sha256": "1dza1kv7s7zjw56shr6bi79vqziabihad6qjrf92p24p0yzzfwsl", "depends": ["ChAMPdata", "DMRcate", "DNAcopy", "DT", "GenomicRanges", "Hmisc", "Illumina450ProbeVariants_db", "IlluminaHumanMethylation450kmanifest", "IlluminaHumanMethylationEPICanno_ilm10b4_hg19", "IlluminaHumanMethylationEPICmanifest", "RColorBrewer", "RPMM", "bumphunter", "combinat", "dendextend", "doParallel", "ggplot2", "globaltest", "goseq", "illuminaio", "impute", "isva", "limma", "marray", "matrixStats", "minfi", "missMethyl", "plotly", "plyr", "preprocessCore", "prettydoc", "quadprog", "qvalue", "rmarkdown", "shiny", "shinythemes", "sva", "wateRmelon"] }, "ChIPComp": { "name": "ChIPComp", "version": "1.38.0", "sha256": "0j5pq8l1azr9abfmnnycy1nkqxy19r4q5pjda45xwsmiz94b543l", "depends": ["BSgenome_Hsapiens_UCSC_hg19", "BSgenome_Mmusculus_UCSC_mm9", "BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "limma", "rtracklayer"] }, "ChIPQC": { "name": "ChIPQC", "version": "1.44.0", "sha256": "1zmxyh9a26niix1rch1xl8imc4fwzjbdbbfbcq14hqhdjha0g95p", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "DiffBind", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "TxDb_Celegans_UCSC_ce6_ensGene", "TxDb_Dmelanogaster_UCSC_dm3_ensGene", "TxDb_Hsapiens_UCSC_hg18_knownGene", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Mmusculus_UCSC_mm10_knownGene", "TxDb_Mmusculus_UCSC_mm9_knownGene", "TxDb_Rnorvegicus_UCSC_rn4_ensGene", "chipseq", "ggplot2", "gtools", "reshape2"] }, "ChIPXpress": { "name": "ChIPXpress", "version": "1.52.0", "sha256": "1qf6pbbypg9889p3lpbmackb0saisq6v4d0vp7l8ngc47rfwzaba", "depends": ["Biobase", "ChIPXpressData", "GEOquery", "affy", "biganalytics", "bigmemory", "frma"] }, "ChIPanalyser": { "name": "ChIPanalyser", "version": "1.30.0", "sha256": "1v3wb8v54vj2q3dqr5xgma6l93qq2b20vfgh0q5r61vgzkzr9j28", "depends": ["BSgenome", "BiocManager", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "ROCR", "RcppRoll", "S4Vectors", "rtracklayer"] }, "ChIPexoQual": { "name": "ChIPexoQual", "version": "1.32.0", "sha256": "1i5ribbhamszq0nllgjqvlii4psypp2qrn81ln8q55ilysv76myv", "depends": ["BiocParallel", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "biovizBase", "broom", "data_table", "dplyr", "ggplot2", "hexbin", "rmarkdown", "scales", "viridis"] }, "ChIPpeakAnno": { "name": "ChIPpeakAnno", "version": "3.42.0", "sha256": "0a2f36bwg287jif8yjhy9q6mr6ilwzm5r425g22sdhghfba8i2gh", "depends": ["AnnotationDbi", "BiocGenerics", "Biostrings", "DBI", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "InteractionSet", "KEGGREST", "RBGL", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VennDiagram", "biomaRt", "data_table", "dplyr", "ensembldb", "ggplot2", "graph", "matrixStats", "multtest", "pwalign", "regioneR", "rtracklayer", "scales", "stringr", "tibble", "tidyr", "universalmotif"] }, "ChIPseeker": { "name": "ChIPseeker", "version": "1.44.0", "sha256": "1agxgvm78wvsirvgk3azqgdqa18k6li78h0zki2fzvmzw7qfzswm", "depends": ["AnnotationDbi", "BiocGenerics", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "TxDb_Hsapiens_UCSC_hg19_knownGene", "aplot", "boot", "dplyr", "enrichplot", "ggplot2", "gplots", "gtools", "magrittr", "plotrix", "rlang", "rtracklayer", "scales", "tibble", "yulab_utils"] }, "ChIPseqR": { "name": "ChIPseqR", "version": "1.62.0", "sha256": "061kq36azgcyx38n58ibrjx4c2wmz9vb9p75ql4x1wchwidfx8zw", "depends": ["BiocGenerics", "Biostrings", "GenomicRanges", "HilbertVis", "IRanges", "S4Vectors", "ShortRead", "fBasics", "timsac"] }, "ChIPsim": { "name": "ChIPsim", "version": "1.62.0", "sha256": "10iz3sxc2qhwjwm2hbnxdzg5ppp6frccfi7m95mg3cpwdwwicm6q", "depends": ["Biostrings", "IRanges", "ShortRead", "XVector"] }, "ChemmineOB": { "name": "ChemmineOB", "version": "1.46.0", "sha256": "0z156k7anzl0xcbch6lcg8z3dkkfy6901x8hl3wsshf6rl9ibahz", "depends": ["BH", "BiocGenerics", "Rcpp", "zlibbioc"] }, "ChemmineR": { "name": "ChemmineR", "version": "3.60.0", "sha256": "0kvg14g4mj8dsyw1ksmgqf5a0dx791px0vf61fmbi5sx67ncirf6", "depends": ["BH", "BiocGenerics", "DBI", "DT", "RCurl", "Rcpp", "base64enc", "digest", "ggplot2", "gridExtra", "jsonlite", "png", "rjson", "rsvg", "stringi"] }, "Chicago": { "name": "Chicago", "version": "1.36.0", "sha256": "0hq96svbcx98gss5wf068rmpz4x85n4k5vf9pd4ips2yzy9454vf", "depends": ["Delaporte", "Hmisc", "MASS", "data_table", "matrixStats"] }, "ChromHeatMap": { "name": "ChromHeatMap", "version": "1.62.0", "sha256": "0d7iwwdvvlfkmpk74vrhw7yh713sd7v01aa7hjq984y071dl4sai", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "GenomicRanges", "IRanges", "annotate", "rtracklayer"] }, "ChromSCape": { "name": "ChromSCape", "version": "1.17.0", "sha256": "1nvm20qh3mzgimp175ykx0z50vzc0wsnb16lwpk5pik8r8yaks7z", "depends": ["BiocParallel", "ConsensusClusterPlus", "DT", "DelayedArray", "GenomicRanges", "IRanges", "Matrix", "Rcpp", "Rsamtools", "Rtsne", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "batchelor", "colorRamps", "colourpicker", "coop", "dplyr", "edgeR", "forcats", "fs", "gggenes", "ggplot2", "ggrepel", "gridExtra", "irlba", "jsonlite", "kableExtra", "matrixTests", "msigdbr", "plotly", "qs", "qualV", "rlist", "rtracklayer", "scater", "scran", "shiny", "shinyFiles", "shinyWidgets", "shinycssloaders", "shinydashboard", "shinydashboardPlus", "shinyhelper", "shinyjs", "stringdist", "stringr", "tibble", "tidyr", "umap", "viridis"] }, "CircSeqAlignTk": { "name": "CircSeqAlignTk", "version": "1.10.0", "sha256": "12cqzc5l8i3jx6g8b6l9ijrr4xym7ahzk3y4yhg6km2mw84b4rh3", "depends": ["BiocGenerics", "Biostrings", "IRanges", "R_utils", "Rbowtie2", "Rhisat2", "Rsamtools", "S4Vectors", "ShortRead", "dplyr", "ggplot2", "htmltools", "magrittr", "plotly", "rlang", "shiny", "shinyFiles", "shinyjs", "tidyr"] }, "CiteFuse": { "name": "CiteFuse", "version": "1.20.0", "sha256": "07ssm67i9dqw40gj2pr3n7k3rfp7g18h8ym6dyqy84zs0bnhh1rk", "depends": ["Matrix", "Rcpp", "Rtsne", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "compositions", "cowplot", "dbscan", "ggplot2", "ggraph", "ggridges", "gridExtra", "igraph", "mixtools", "pheatmap", "randomForest", "reshape2", "rhdf5", "rlang", "scales", "scran", "uwot"] }, "ClassifyR": { "name": "ClassifyR", "version": "3.12.2", "sha256": "19mw8s260f794qyfhpwzha3bp7bmc00rx2p04j4qjv77s03mcsv0", "depends": ["BiocParallel", "MultiAssayExperiment", "S4Vectors", "broom", "dcanr", "dplyr", "genefilter", "generics", "ggplot2", "ggpubr", "ggupset", "ranger", "reshape2", "rlang", "survival", "tidyr"] }, "CleanUpRNAseq": { "name": "CleanUpRNAseq", "version": "1.2.0", "sha256": "1bkyl0q140hpg1rq5dqgcrg4xdkm1g1sla3cq0g75qj5ggx1n2hj", "depends": ["AnnotationFilter", "BSgenome", "BiocGenerics", "Biostrings", "DESeq2", "GenomeInfoDb", "GenomicRanges", "KernSmooth", "R6", "RColorBrewer", "Rsamtools", "Rsubread", "SummarizedExperiment", "edgeR", "ensembldb", "ggplot2", "ggrepel", "limma", "pheatmap", "qsmooth", "reshape2", "tximport"] }, "Clomial": { "name": "Clomial", "version": "1.44.0", "sha256": "05i8dfbn110ywaqd3d2f6xbl1ra2bax3j0in3fyi360ra3kq62rw", "depends": ["matrixStats", "permute"] }, "CluMSID": { "name": "CluMSID", "version": "1.24.0", "sha256": "0vzam72cqn4mnxvikwazy4gmf3dyygwc5p2gchqc8sn0py4nxmy2", "depends": ["Biobase", "GGally", "MSnbase", "RColorBrewer", "S4Vectors", "ape", "dbscan", "ggplot2", "gplots", "mzR", "network", "plotly", "sna"] }, "ClustAll": { "name": "ClustAll", "version": "1.4.0", "sha256": "059cagw9i9789lqnfz3zr3lz54l95gfjpndzxwsmp2gxdh7b5l7b", "depends": ["ComplexHeatmap", "FactoMineR", "RColorBrewer", "bigstatsr", "circlize", "clValid", "cluster", "doSNOW", "dplyr", "flock", "foreach", "fpc", "ggplot2", "mice", "modeest", "networkD3", "pbapply"] }, "ClustIRR": { "name": "ClustIRR", "version": "1.6.0", "sha256": "0gbafvcbya0g6prnrcz6xpb92f1ykaqfyyal07jwm8cf0ivqmb3c", "depends": ["BH", "Rcpp", "RcppEigen", "RcppParallel", "StanHeaders", "blaster", "dplyr", "future", "future_apply", "ggforce", "ggplot2", "igraph", "posterior", "reshape2", "rstan", "rstantools", "scales", "stringdist", "tidyr", "visNetwork"] }, "ClusterFoldSimilarity": { "name": "ClusterFoldSimilarity", "version": "1.4.0", "sha256": "0479rfz74d5vb299f51vprjd1cjppggi4xss2wh51i3ln9qznj86", "depends": ["BiocParallel", "Matrix", "Seurat", "SeuratObject", "SingleCellExperiment", "cowplot", "dplyr", "ggdendro", "ggplot2", "igraph", "reshape2", "scales"] }, "ClusterJudge": { "name": "ClusterJudge", "version": "1.30.0", "sha256": "1hqlvf253chqalc1vzrfv295g8f2z3qnx7yhxx8pnkm5q2xjc4bb", "depends": ["httr", "infotheo", "jsonlite", "lattice", "latticeExtra"] }, "ClusterSignificance": { "name": "ClusterSignificance", "version": "1.36.0", "sha256": "1pp8g2l6kq4rvki0v895b0q36disasrmwmw8m8pk6k0qwidh1mi0", "depends": ["RColorBrewer", "pracma", "princurve", "scatterplot3d"] }, "CoCiteStats": { "name": "CoCiteStats", "version": "1.80.0", "sha256": "1j67wy8rcwv6z32wkkm0cxr0iqji0hpbrxfzydd9dvb5rf7lbg6c", "depends": ["AnnotationDbi", "org_Hs_eg_db"] }, "CoGAPS": { "name": "CoGAPS", "version": "3.28.0", "sha256": "0i9pj6pwgkb5i3h367hprb8qdi6a0fmd450sij5naw5nbb1j5hks", "depends": ["BH", "BiocParallel", "RColorBrewer", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "cluster", "dplyr", "fgsea", "forcats", "ggplot2", "gplots", "rhdf5", "testthat"] }, "CoSIA": { "name": "CoSIA", "version": "1.8.0", "sha256": "1xkh2nms6pynpaaw1ckkp2d5vgi93m27jxac9js02cxixg1qmc3l", "depends": ["AnnotationDbi", "ExperimentHub", "RColorBrewer", "annotationTools", "biomaRt", "dplyr", "ggplot2", "homologene", "magrittr", "org_Ce_eg_db", "org_Dm_eg_db", "org_Dr_eg_db", "org_Hs_eg_db", "org_Mm_eg_db", "org_Rn_eg_db", "plotly", "readr", "stringr", "tibble", "tidyr", "tidyselect"] }, "Cogito": { "name": "Cogito", "version": "1.14.0", "sha256": "1lv1lckrkydxp6670d7i138v9vhcsprrg56hp98jwab91l4lbgp3", "depends": ["AnnotationDbi", "BiocManager", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "S4Vectors", "TxDb_Mmusculus_UCSC_mm9_knownGene", "entropy", "ggplot2", "jsonlite", "magrittr", "rmarkdown"] }, "ComPrAn": { "name": "ComPrAn", "version": "1.16.0", "sha256": "0pcm5hsjcv87avjpsb0cvybs44042grjwj7vzfscaj9j7iv4cixq", "depends": ["DT", "RColorBrewer", "VennDiagram", "data_table", "dplyr", "forcats", "ggplot2", "magrittr", "purrr", "rio", "rlang", "scales", "shiny", "shinydashboard", "shinyjs", "stringr", "tibble", "tidyr"] }, "ComplexHeatmap": { "name": "ComplexHeatmap", "version": "2.24.1", "sha256": "0ys41vjk1wc23my7yihwzygw8rvi495npy1vpyfw9g9p2ml0xkdj", "depends": ["GetoptLong", "GlobalOptions", "IRanges", "RColorBrewer", "circlize", "clue", "codetools", "colorspace", "digest", "doParallel", "foreach", "matrixStats", "png"] }, "CompoundDb": { "name": "CompoundDb", "version": "1.12.1", "sha256": "1n4ir5hr4clzj6qwxa9aa95msly2hdhcymnjyly81hw9vjbrv461", "depends": ["AnnotationFilter", "Biobase", "BiocGenerics", "BiocParallel", "ChemmineR", "DBI", "IRanges", "MetaboCoreUtils", "MsCoreUtils", "ProtGenerics", "RSQLite", "S4Vectors", "Spectra", "dbplyr", "dplyr", "jsonlite", "stringi", "tibble", "xml2"] }, "ConsensusClusterPlus": { "name": "ConsensusClusterPlus", "version": "1.72.0", "sha256": "0mxz03nyhprahlsban3l6k5wlgsrhg1z8a25y0ndwqfd6w2gvf2a", "depends": ["ALL", "Biobase", "cluster"] }, "CopyNumberPlots": { "name": "CopyNumberPlots", "version": "1.24.0", "sha256": "1avcq4qjgwa9g2f3izvay5cj8vzm7gqp7ivfvmw02k9515bw7zs1", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "SummarizedExperiment", "VariantAnnotation", "cn_mops", "karyoploteR", "regioneR", "rhdf5"] }, "CoreGx": { "name": "CoreGx", "version": "2.12.0", "sha256": "1lqqk19vi8332qrg1iwr5zalhqba5inlgdmywgql3hahak4qhwxx", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "BumpyMatrix", "MatrixGenerics", "MultiAssayExperiment", "S4Vectors", "SummarizedExperiment", "bench", "checkmate", "crayon", "data_table", "glue", "lsa", "piano", "rlang"] }, "Cormotif": { "name": "Cormotif", "version": "1.54.0", "sha256": "0mirma6qy7ha1yf1gl0fpdndw1v4s3is1yr3ibm3fyw3s7gxanij", "depends": ["affy", "limma"] }, "CoverageView": { "name": "CoverageView", "version": "1.46.0", "sha256": "1x6gsslsvfab75p8pcbbffgzzqh94q1awa31mv34j25a5hz59r38", "depends": ["GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "rtracklayer"] }, "CrispRVariants": { "name": "CrispRVariants", "version": "1.36.0", "sha256": "0f8fbzl6hllac57ydlxns56aqcrla1pd5rkpdvxpy45294f79vm2", "depends": ["AnnotationDbi", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "ggplot2", "gridExtra", "reshape2"] }, "CuratedAtlasQueryR": { "name": "CuratedAtlasQueryR", "version": "1.6.0", "sha256": "1sjxd132r7l9p56yiakkcyysbbvw5hy0j4l3kg6liskyp6cridxx", "depends": ["BiocGenerics", "DBI", "HDF5Array", "S4Vectors", "Seurat", "SeuratObject", "SingleCellExperiment", "SummarizedExperiment", "assertthat", "cli", "dbplyr", "dplyr", "duckdb", "glue", "httr", "purrr", "rlang", "stringr", "tibble"] }, "CyTOFpower": { "name": "CyTOFpower", "version": "1.14.0", "sha256": "0a4qr7b095mvv9z0f75cja16zm73gpr888djn9vzmckmrmddns7f", "depends": ["CytoGLMM", "DT", "SummarizedExperiment", "diffcyt", "dplyr", "ggplot2", "magrittr", "rlang", "shiny", "shinyFeedback", "shinyMatrix", "shinyjs", "tibble", "tidyr"] }, "CytoDx": { "name": "CytoDx", "version": "1.28.0", "sha256": "0h6vghvai24g1nd0v50pm7avd3lgi9kld0j1iqb49acv8f7kj7cs", "depends": ["doParallel", "dplyr", "flowCore", "glmnet", "rpart", "rpart_plot"] }, "CytoGLMM": { "name": "CytoGLMM", "version": "1.16.1", "sha256": "1c7wyvqh9if4zbcn6m73fa4dk04bbp6nb8jdd0i5psga50bjm0c9", "depends": ["BiocParallel", "MASS", "Matrix", "RColorBrewer", "caret", "cowplot", "doParallel", "dplyr", "factoextra", "flexmix", "ggplot2", "ggrepel", "logging", "magrittr", "mbest", "pheatmap", "rlang", "stringr", "strucchange", "tibble", "tidyr"] }, "CytoMDS": { "name": "CytoMDS", "version": "1.4.0", "sha256": "0a3lzb875395brq1xrpm8kl24arzhaqjn5bj2v23ls8pzr2mbgby", "depends": ["Biobase", "BiocParallel", "CytoPipeline", "flowCore", "ggforce", "ggplot2", "ggrepel", "patchwork", "pracma", "reshape2", "rlang", "smacof", "transport", "withr"] }, "CytoML": { "name": "CytoML", "version": "2.20.0", "sha256": "0xrwpxn7zbcvj6ng56wp8vw74jr50nz6qab0z8fb0hlzfa0dnpdw", "depends": ["BH", "Biobase", "RBGL", "RProtoBufLib", "Rgraphviz", "Rhdf5lib", "XML", "cpp11", "cytolib", "data_table", "dplyr", "flowCore", "flowWorkspace", "ggcyto", "graph", "jsonlite", "openCyto", "tibble", "yaml"] }, "CytoPipeline": { "name": "CytoPipeline", "version": "1.8.0", "sha256": "1rr9s6l9m4w165gjsz3k131q9pl9sc8jm30cznm7vignf8aq6g2v", "depends": ["BiocFileCache", "BiocParallel", "PeacoQC", "diagram", "flowAI", "flowCore", "ggcyto", "ggplot2", "jsonlite", "rlang", "scales", "withr"] }, "CytoPipelineGUI": { "name": "CytoPipelineGUI", "version": "1.6.0", "sha256": "1icvjw517f4pip67liihad9vnfhzq5p8n21vsfcxlypys78lpc2x", "depends": ["CytoPipeline", "flowCore", "ggplot2", "plotly", "shiny"] }, "DAMEfinder": { "name": "DAMEfinder", "version": "1.20.0", "sha256": "17yb21gs9124ii65m95s6v6irmlfhqzd81sq03vzgl5k7ajkl7dc", "depends": ["BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "bumphunter", "cowplot", "ggplot2", "limma", "plyr", "readr", "reshape2", "stringr"] }, "DAPAR": { "name": "DAPAR", "version": "1.40.0", "sha256": "1v1bv7q161rd52ynp9xv333li41c3pxzm09wafpbg4hf98knnpbl", "depends": ["Biobase", "DAPARdata", "MSnbase", "foreach", "highcharter"] }, "DART": { "name": "DART", "version": "1.56.0", "sha256": "0qkdh3112j04vpxyqv8k1sznrmx34nayg8qdrz0b43kix9my6ffn", "depends": ["igraph"] }, "DCATS": { "name": "DCATS", "version": "1.6.0", "sha256": "0pia4rbg4mvxv2p175vg23hrclcnzxjfbiq3xs41r50xb1wq175x", "depends": ["MCMCpack", "aod", "e1071", "matrixStats", "robustbase"] }, "DECIPHER": { "name": "DECIPHER", "version": "3.4.0", "sha256": "1llz1p0sikdqdc1505whnsbr68k4r3lq6sc7fgjaa5dybycrmkwy", "depends": ["Biostrings", "DBI", "IRanges", "S4Vectors", "XVector"] }, "DEFormats": { "name": "DEFormats", "version": "1.36.0", "sha256": "011mbkvfmrdgrahp046yd1a5cc0hqpicfjg4hwak5nnliai7i9yh", "depends": ["DESeq2", "GenomicRanges", "S4Vectors", "SummarizedExperiment", "checkmate", "data_table", "edgeR"] }, "DEGraph": { "name": "DEGraph", "version": "1.60.0", "sha256": "0qaxw5kb7qp11dlyb8rdajvhx04qnai16w6qckq64abn7g21lm5h", "depends": ["KEGGgraph", "NCIgraph", "RBGL", "R_methodsS3", "R_utils", "Rgraphviz", "graph", "lattice", "mvtnorm", "rrcov"] }, "DEGreport": { "name": "DEGreport", "version": "1.44.0", "sha256": "142h3kswqr8v5mcsj35v094cq3vgx2p0019v3nmycmsxidfw7p59", "depends": ["Biobase", "BiocGenerics", "ComplexHeatmap", "ConsensusClusterPlus", "DESeq2", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "broom", "circlize", "cluster", "cowplot", "dendextend", "dplyr", "edgeR", "ggdendro", "ggplot2", "ggrepel", "knitr", "logging", "magrittr", "psych", "reshape", "rlang", "scales", "stringi", "stringr", "tibble", "tidyr"] }, "DEGseq": { "name": "DEGseq", "version": "1.62.0", "sha256": "1903v9bfbaadr24g1c65qvb98qv1222lmmx6x3hni19cpsi233nz", "depends": ["qvalue"] }, "DELocal": { "name": "DELocal", "version": "1.8.0", "sha256": "0hinzs1220hs7qfjv5na9cn7929wbrnvr409ay0vgphzkh92w30z", "depends": ["DESeq2", "SummarizedExperiment", "dplyr", "ggplot2", "limma", "matrixStats", "reshape2"] }, "DEP": { "name": "DEP", "version": "1.30.0", "sha256": "1cf30pf5j51rhgp1i56w5j83yqpblk5pnigw1qxzm6d70277a8yg", "depends": ["ComplexHeatmap", "DT", "MSnbase", "RColorBrewer", "SummarizedExperiment", "assertthat", "circlize", "cluster", "dplyr", "fdrtool", "ggplot2", "ggrepel", "gridExtra", "imputeLCMD", "limma", "purrr", "readr", "rmarkdown", "shiny", "shinydashboard", "tibble", "tidyr", "vsn"] }, "DEScan2": { "name": "DEScan2", "version": "1.28.0", "sha256": "1ci8bwpgwk71kcgy1sqabapxbr5fj6nyn8wr2kyzn9lc1v387qkb", "depends": ["BiocGenerics", "BiocParallel", "ChIPpeakAnno", "DelayedArray", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rcpp", "RcppArmadillo", "S4Vectors", "SummarizedExperiment", "data_table", "glue", "plyr", "rtracklayer"] }, "DESeq2": { "name": "DESeq2", "version": "1.48.1", "sha256": "1gk5kk9yjjwa2laiamwcn8n1j2497gbrhzczgsfg58fnwfxcbs1q", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "GenomicRanges", "IRanges", "MatrixGenerics", "Rcpp", "RcppArmadillo", "S4Vectors", "SummarizedExperiment", "ggplot2", "locfit", "matrixStats"] }, "DESpace": { "name": "DESpace", "version": "2.0.0", "sha256": "195by5l6iiga8xcvry11x9x0303f3h47i5qf4a32f2n3hzb9m8k7", "depends": ["BiocGenerics", "BiocParallel", "Matrix", "S4Vectors", "SpatialExperiment", "SummarizedExperiment", "assertthat", "data_table", "dplyr", "edgeR", "ggforce", "ggnewscale", "ggplot2", "limma", "patchwork", "scales", "scuttle", "sf", "spatstat_explore", "spatstat_geom", "terra"] }, "DEWSeq": { "name": "DEWSeq", "version": "1.22.0", "sha256": "042534cn0hczfzsh7dk5g3rsskkqf2mbs217j2gqlvblj84vnl35", "depends": ["BiocGenerics", "BiocParallel", "DESeq2", "GenomeInfoDb", "GenomicRanges", "R_utils", "S4Vectors", "SummarizedExperiment", "data_table"] }, "DEXSeq": { "name": "DEXSeq", "version": "1.54.1", "sha256": "15jr6g339dljpryixbxfy4srr8qjwdqs2jfj86lhw9lfslwwj80q", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocParallel", "DESeq2", "GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "SummarizedExperiment", "biomaRt", "genefilter", "geneplotter", "hwriter", "statmod", "stringr"] }, "DEqMS": { "name": "DEqMS", "version": "1.26.0", "sha256": "19ryqbyng01ykjiphykrd57z1rh2gahzglb7z28kn64paamap2jc", "depends": ["dplyr", "ggplot2", "limma", "matrixStats"] }, "DEsingle": { "name": "DEsingle", "version": "1.28.0", "sha256": "1djicbxx4j0nm5rydfn1yxcimvnldzxffpavcyw25f9fxlb05yb2", "depends": ["BiocParallel", "MASS", "Matrix", "VGAM", "bbmle", "gamlss", "maxLik", "pscl"] }, "DEsubs": { "name": "DEsubs", "version": "1.34.0", "sha256": "03y7pc094s9y36x6mm0xph6xj0z7ivzzs8awwc44pjs24p0776ic", "depends": ["DESeq2", "EBSeq", "Matrix", "NBPSeq", "RBGL", "circlize", "edgeR", "ggplot2", "graph", "igraph", "jsonlite", "limma", "locfit", "pheatmap"] }, "DExMA": { "name": "DExMA", "version": "1.16.0", "sha256": "077y1vb8rnakqbgjhfb2brj3vx8m3hv1wqyxv60dz0dhxx7b2nvz", "depends": ["Biobase", "DExMAdata", "GEOquery", "RColorBrewer", "bnstruct", "impute", "limma", "pheatmap", "plyr", "scales", "snpStats", "sva", "swamp"] }, "DFP": { "name": "DFP", "version": "1.66.0", "sha256": "155v02mi40d81hddiv9750md91gb3y6qyjaif97vxahcr8f8lx8w", "depends": ["Biobase"] }, "DFplyr": { "name": "DFplyr", "version": "1.2.0", "sha256": "1n39rnvmr4hvhq4fpwisvib7xkzb1gdrv84jm4ccwzm4yrxdpb7y", "depends": ["BiocGenerics", "S4Vectors", "dplyr", "rlang", "tidyselect"] }, "DMCFB": { "name": "DMCFB", "version": "1.22.1", "sha256": "1lw75h7iki6v66zrkcrwm5xi396b2xvaxsn53fa9nijgj91nwyj8", "depends": ["BiocParallel", "GenomicRanges", "IRanges", "MASS", "S4Vectors", "SummarizedExperiment", "arm", "benchmarkme", "data_table", "fastDummies", "matrixStats", "rtracklayer", "speedglm", "tibble"] }, "DMCHMM": { "name": "DMCHMM", "version": "1.30.1", "sha256": "1xanic84pa5hi3zzqkklfc8awpyn04831r02di576fw037aski9c", "depends": ["BiocParallel", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "calibrate", "fdrtool", "multcomp", "rtracklayer"] }, "DMRScan": { "name": "DMRScan", "version": "1.30.0", "sha256": "1ln100csirxyvy3z0sn7k1vqmhb6rgc5y6ngvg335b6rhfwnqs2s", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "MASS", "Matrix", "RcppRoll", "mvtnorm"] }, "DMRcaller": { "name": "DMRcaller", "version": "1.40.0", "sha256": "04cclx7p9clnraj6d14wsx60h6wlxs923dzqx287rxfkj5a61723", "depends": ["GenomicRanges", "IRanges", "Rcpp", "RcppRoll", "S4Vectors", "betareg"] }, "DMRcate": { "name": "DMRcate", "version": "3.4.0", "sha256": "1q6z83v9s1rm0rllda8qpln876mif5v9jqjw7x8dqb561q9plg7p", "depends": ["AnnotationHub", "ExperimentHub", "GenomeInfoDb", "GenomicRanges", "Gviz", "IRanges", "S4Vectors", "SummarizedExperiment", "biomaRt", "bsseq", "edgeR", "limma", "minfi", "missMethyl", "plyr"] }, "DNABarcodeCompatibility": { "name": "DNABarcodeCompatibility", "version": "1.24.0", "sha256": "04pfilpvbp3n3a021x6i22y2lx05l99xlxq2qq71hzvq8icf7l2d", "depends": ["BH", "Rcpp", "dplyr", "numbers", "purrr", "stringr", "tidyr"] }, "DNABarcodes": { "name": "DNABarcodes", "version": "1.38.0", "sha256": "1v2snhg4bx9sdy75vipv5ik64r437kfb7bbi9cqncg4i81pgni1x", "depends": ["BH", "Matrix", "Rcpp"] }, "DNAcopy": { "name": "DNAcopy", "version": "1.82.0", "sha256": "1r9yppn98qphkj97v94hkg9llw25xxafdh7f87xs9n5f07l186rr", "depends": [] }, "DNAcycP2": { "name": "DNAcycP2", "version": "1.0.0", "sha256": "1p5wfkawsa5d0q4xksy6k5sc78xyjq0c62wgn8nzsgc5yqd17ww3", "depends": ["basilisk", "reticulate"] }, "DNAfusion": { "name": "DNAfusion", "version": "1.10.0", "sha256": "038f81458s3329rgsbjfn0hibj8awiybgglxlgdj56xkph0757d6", "depends": ["BiocBaseUtils", "BiocGenerics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "TxDb_Hsapiens_UCSC_hg38_knownGene", "bamsignals"] }, "DNAshapeR": { "name": "DNAshapeR", "version": "1.36.0", "sha256": "0c2jdwy42vlpyv18628df4b1byd1mkrqp1zdyqc0qs1fv33ig3zc", "depends": ["Biostrings", "GenomicRanges", "Rcpp", "fields"] }, "DOSE": { "name": "DOSE", "version": "4.2.0", "sha256": "1hs3f7mhzc3pf2f8xyp38430l4zqq2vkjx52zwavnk1dqpp8cbdh", "depends": ["AnnotationDbi", "BiocParallel", "GOSemSim", "fgsea", "ggplot2", "qvalue", "reshape2", "yulab_utils"] }, "DRIMSeq": { "name": "DRIMSeq", "version": "1.36.0", "sha256": "1sfm0wzjypbdvvx97jk5qbnx2a1bbmsccsvjn5imziqh7hil7cbv", "depends": ["BiocGenerics", "BiocParallel", "GenomicRanges", "IRanges", "MASS", "S4Vectors", "edgeR", "ggplot2", "limma", "reshape2"] }, "DSS": { "name": "DSS", "version": "2.56.0", "sha256": "02811qmnpj2jn85mhj1whddn2pj16ymylz3nj8bmw95z3n2dsjk7", "depends": ["Biobase", "BiocParallel", "bsseq"] }, "DTA": { "name": "DTA", "version": "2.54.0", "sha256": "1jfdiisj2f77mgkyp7qgaf9zysj2nhbfrczqsnkws0c4mpzhiaz1", "depends": ["LSD", "scatterplot3d"] }, "DaMiRseq": { "name": "DaMiRseq", "version": "2.20.0", "sha256": "03953d0j4r9bh79wkcs9781nana3cwa9yf59vl64p87ng9xwbx08", "depends": ["DESeq2", "EDASeq", "FSelector", "FactoMineR", "Hmisc", "MASS", "RColorBrewer", "RSNNS", "SummarizedExperiment", "arm", "caret", "corrplot", "e1071", "edgeR", "ggplot2", "ineq", "kknn", "limma", "lubridate", "pheatmap", "pls", "plsVarSel", "plyr", "randomForest", "reshape2", "sva"] }, "Damsel": { "name": "Damsel", "version": "1.4.0", "sha256": "1hd923bx1ypvdgyixyd5bgshbc3ikikbx3nmvmnqicypalxnm8cz", "depends": ["AnnotationDbi", "Biostrings", "ComplexHeatmap", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "Rsamtools", "Rsubread", "dplyr", "edgeR", "ggbio", "ggplot2", "goseq", "magrittr", "patchwork", "plyranges", "reshape2", "rlang", "stringr", "tidyr"] }, "DeMAND": { "name": "DeMAND", "version": "1.38.0", "sha256": "1w3qpiv7zj603c3iqasi702mx3sbxi6rkyj3q024wjwsbb1114n4", "depends": ["KernSmooth"] }, "DeMixT": { "name": "DeMixT", "version": "1.24.0", "sha256": "1cagx7i2vyzjyjh31zk23r6frnqqmj31ak5i1anw1qslqibwsb9m", "depends": ["DSS", "KernSmooth", "Rcpp", "SummarizedExperiment", "base64enc", "dendextend", "ggplot2", "knitr", "matrixStats", "matrixcalc", "psych", "rmarkdown", "sva", "truncdist"] }, "DeconRNASeq": { "name": "DeconRNASeq", "version": "1.50.0", "sha256": "06dkxdikfgiay72z9p0kmk8bayvdbrg641cl39nwk109dms0vc6f", "depends": ["ggplot2", "limSolve", "pcaMethods"] }, "DeconvoBuddies": { "name": "DeconvoBuddies", "version": "1.0.0", "sha256": "1qaajr5rm7qkqg7kg8qnqbaq7ijnzn83l4vncjf1hz4c5j8vzw1s", "depends": ["AnnotationHub", "BiocFileCache", "ExperimentHub", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "dplyr", "ggplot2", "matrixStats", "purrr", "rafalib", "reshape2", "scran", "spatialLIBD", "stringr", "tibble"] }, "DeepPINCS": { "name": "DeepPINCS", "version": "1.16.0", "sha256": "0sc72ghyrhr29xhyhwgnq0sqqdn9xlwkv3p3mfyrbb0rxrkm07zs", "depends": ["CatEncoders", "PRROC", "keras", "matlab", "purrr", "rcdk", "reticulate", "stringdist", "tensorflow", "tokenizers", "ttgsea", "webchem"] }, "DeepTarget": { "name": "DeepTarget", "version": "1.2.0", "sha256": "1yhyjspnfk3q3z4jny1lpbbvj62h7d8ka58xcwzj8ckp6pg04dp4", "depends": ["BiocParallel", "depmap", "dplyr", "fgsea", "ggplot2", "ggpubr", "pROC", "readr", "stringr"] }, "DegCre": { "name": "DegCre", "version": "1.4.0", "sha256": "044kr8ic0rjd8l4y5ypdxf4ajh6q8w10p825acp4qn09fh453k4x", "depends": ["BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicRanges", "IRanges", "InteractionSet", "S4Vectors", "TxDb_Hsapiens_UCSC_hg38_knownGene", "org_Hs_eg_db", "plotgardener", "qvalue"] }, "DegNorm": { "name": "DegNorm", "version": "1.18.0", "sha256": "1a4yxwj2jfjp06sw3kyh6zyh8h7f83prabp9h0zl3zzbp6fh44pn", "depends": ["GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rcpp", "RcppArmadillo", "Rsamtools", "S4Vectors", "data_table", "doParallel", "foreach", "ggplot2", "heatmaply", "plotly", "plyr", "txdbmaker", "viridis"] }, "DelayedArray": { "name": "DelayedArray", "version": "0.34.1", "sha256": "09fx4gq0yx9k0qfxj6596dw4kn9h1wnzxwn142ld429vsn4gp3z7", "depends": ["BiocGenerics", "IRanges", "Matrix", "MatrixGenerics", "S4Arrays", "S4Vectors", "SparseArray"] }, "DelayedDataFrame": { "name": "DelayedDataFrame", "version": "1.24.0", "sha256": "130qd102wyh9chdjsw1nbp5lzigzaajz429zslwjpbwvi9vd72zd", "depends": ["BiocGenerics", "DelayedArray", "S4Vectors"] }, "DelayedMatrixStats": { "name": "DelayedMatrixStats", "version": "1.30.0", "sha256": "0mwflq5rdb172w2pjd0rkdivinilgdvh7r7zm0iqxxsw1imkj6sp", "depends": ["DelayedArray", "IRanges", "Matrix", "MatrixGenerics", "S4Vectors", "SparseArray", "sparseMatrixStats"] }, "DelayedRandomArray": { "name": "DelayedRandomArray", "version": "1.16.0", "sha256": "1l1m2lvzpgryw2d41gy2issr4lrxrrfqg9mypj18wwgyd6p6bfvi", "depends": ["BH", "DelayedArray", "Rcpp", "SparseArray", "dqrng"] }, "DelayedTensor": { "name": "DelayedTensor", "version": "1.14.0", "sha256": "1pqvabsdfg21axx3w12gg6kjadinwmrcrvr0jadzmxr8p816vprj", "depends": ["BiocSingular", "DelayedArray", "DelayedRandomArray", "HDF5Array", "Matrix", "S4Arrays", "SparseArray", "einsum", "irlba", "rTensor"] }, "DepInfeR": { "name": "DepInfeR", "version": "1.12.0", "sha256": "1cl6bzp5hs10yh9r0rp7ww251farwr0w49izgwy8pah9x7ran52z", "depends": ["BiocParallel", "glmnet", "matrixStats"] }, "DepecheR": { "name": "DepecheR", "version": "1.24.0", "sha256": "1x00w0qs4pl5j6q7pr7iq83fw5frk9yk5bysr87sv6qpc84afhz4", "depends": ["ClusterR", "FNN", "MASS", "Rcpp", "RcppEigen", "beanplot", "collapse", "doSNOW", "dplyr", "foreach", "ggplot2", "gmodels", "gplots", "matrixStats", "mixOmics", "moments", "reshape2", "robustbase", "viridis"] }, "DiffBind": { "name": "DiffBind", "version": "3.18.0", "sha256": "1dcdslb8zd3i5fpkn5nmg36gmil3q8g1vzjgbq17hif6gnah8bgi", "depends": ["BiocParallel", "DESeq2", "GenomicAlignments", "GenomicRanges", "GreyListChIP", "IRanges", "RColorBrewer", "Rcpp", "Rhtslib", "Rsamtools", "S4Vectors", "SummarizedExperiment", "amap", "apeglm", "ashr", "dplyr", "ggplot2", "ggrepel", "gplots", "lattice", "limma", "locfit", "systemPipeR"] }, "DiffLogo": { "name": "DiffLogo", "version": "2.32.0", "sha256": "0rkwlsqqc1d2zw25415cj43033vh722jpgglr8k4ljbp99z5yydn", "depends": ["cba"] }, "DifferentialRegulation": { "name": "DifferentialRegulation", "version": "2.6.0", "sha256": "0jjpaviyfms733m0v0lfig40rqg1j0jw3ifz8vd6knk8bcr3227q", "depends": ["BANDITS", "MASS", "Matrix", "Rcpp", "RcppArmadillo", "SingleCellExperiment", "SummarizedExperiment", "data_table", "doParallel", "doRNG", "foreach", "ggplot2", "gridExtra", "tximport"] }, "Dino": { "name": "Dino", "version": "1.14.0", "sha256": "1f75740fbnzkl4qmgr8vkc79xrj4cxy7rfwl3hmpjv28wwvnbmgl", "depends": ["BiocParallel", "BiocSingular", "Matrix", "S4Vectors", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "matrixStats", "scran"] }, "Director": { "name": "Director", "version": "1.34.0", "sha256": "0xvpr1j36q46dlfympsivv5kxxnhskywc4fhxk0010yvx92ngpsw", "depends": ["htmltools"] }, "DirichletMultinomial": { "name": "DirichletMultinomial", "version": "1.50.0", "sha256": "0v4ch5nrz6kf6scxc98w9jdalmgllzy9qh35pfdx0z7wbbklk9z8", "depends": ["BiocGenerics", "IRanges", "S4Vectors"] }, "DiscoRhythm": { "name": "DiscoRhythm", "version": "1.24.0", "sha256": "0i6l1q5xj3qn6pqzqdfpax1phh8c9vfan6k12vydlvbx2q14m1pb", "depends": ["BiocGenerics", "BiocStyle", "DT", "MetaCycle", "S4Vectors", "SummarizedExperiment", "UpSetR", "VennDiagram", "broom", "data_table", "dplyr", "ggExtra", "ggplot2", "gridExtra", "heatmaply", "kableExtra", "knitr", "magick", "matrixStats", "matrixTests", "plotly", "reshape2", "rmarkdown", "shiny", "shinyBS", "shinycssloaders", "shinydashboard", "shinyjs", "viridis", "zip"] }, "DominoEffect": { "name": "DominoEffect", "version": "1.28.0", "sha256": "1x5pik4wj9b3zbmhd15v3pn8grhz1cn47d4cslwc8pgl7s3rzcwi", "depends": ["AnnotationDbi", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "SummarizedExperiment", "VariantAnnotation", "biomaRt", "data_table", "pwalign"] }, "Doscheda": { "name": "Doscheda", "version": "1.30.0", "sha256": "03qvng07nv346gn6df3bp1574yiampl26zjcln4by7f0fjdisfx5", "depends": ["DT", "affy", "calibrate", "corrgram", "drc", "ggplot2", "gridExtra", "httr", "jsonlite", "limma", "matrixStats", "prodlim", "readxl", "reshape2", "shiny", "shinydashboard", "stringr", "vsn"] }, "DriverNet": { "name": "DriverNet", "version": "1.48.0", "sha256": "03cfjq0j72q2aqzkaz4qg2idmb4dfhi0grhd6d1m98q3xdnw37dw", "depends": [] }, "DropletUtils": { "name": "DropletUtils", "version": "1.28.1", "sha256": "1fg8m5fcwqcdp81q0vbm7sq4c274zhnbami1c4g71rd712xhjnd0", "depends": ["BH", "BiocGenerics", "BiocParallel", "DelayedArray", "DelayedMatrixStats", "GenomicRanges", "HDF5Array", "IRanges", "Matrix", "R_utils", "Rcpp", "Rhdf5lib", "S4Vectors", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "beachmat", "dqrng", "edgeR", "rhdf5", "scuttle"] }, "DrugVsDisease": { "name": "DrugVsDisease", "version": "2.50.0", "sha256": "0svqjmlkxfxwians5nmjhwzcyfq3p99ajywamhp9shsqjfqmry3x", "depends": ["ArrayExpress", "BiocGenerics", "DrugVsDiseasedata", "GEOquery", "RUnit", "affy", "annotate", "biomaRt", "cMap2data", "hgu133a2_db", "hgu133a_db", "hgu133plus2_db", "limma", "qvalue", "xtable"] }, "Dune": { "name": "Dune", "version": "1.20.0", "sha256": "1xk27ywjd87qbbbzh1lwrbwzkq05hb3p3wz54i7p52rc5s3isp48", "depends": ["BiocParallel", "RColorBrewer", "SummarizedExperiment", "aricode", "dplyr", "gganimate", "ggplot2", "magrittr", "purrr", "tidyr"] }, "DuplexDiscovereR": { "name": "DuplexDiscovereR", "version": "1.2.0", "sha256": "1nm7jjrgvpivn4hfffridm5r0m933qwldvgbmqfxqn0hhczx335q", "depends": ["Biostrings", "GenomicAlignments", "GenomicRanges", "Gviz", "InteractionSet", "dplyr", "ggsci", "igraph", "purrr", "rlang", "rtracklayer", "scales", "stringr", "tibble", "tidyr"] }, "DynDoc": { "name": "DynDoc", "version": "1.86.0", "sha256": "08dlkhm9nw5xbc1qi4chknx0lalwnnv69w9jgsmr7qf554xvq54q", "depends": [] }, "EBImage": { "name": "EBImage", "version": "4.50.0", "sha256": "05ndq0dwdwprl076g866zayjrk85ha3vihm9qh4dchwkmn2rm9hi", "depends": ["BiocGenerics", "RCurl", "abind", "fftwtools", "htmltools", "htmlwidgets", "jpeg", "locfit", "png", "tiff"] }, "EBSEA": { "name": "EBSEA", "version": "1.36.0", "sha256": "19px1nsrny4v203f65qs3xbgrf1n6l9vlmpmi02b1sy8fg39wd28", "depends": ["DESeq2", "EmpiricalBrownsMethod"] }, "EBSeq": { "name": "EBSeq", "version": "2.6.0", "sha256": "03r31hba6qiy7x11cxlhy2gwgk6b3biz9r9j9y8mc9c6vh9h6q0h", "depends": ["BH", "Rcpp", "RcppEigen", "blockmodeling", "gplots", "testthat"] }, "EBarrays": { "name": "EBarrays", "version": "2.72.0", "sha256": "04p4zxx4z5hzgw957rl3zwfpy8yrsaj7jab70xz05i1nc315l0kp", "depends": ["Biobase", "cluster", "lattice"] }, "EBcoexpress": { "name": "EBcoexpress", "version": "1.52.0", "sha256": "0a2jrs8w5a69581w0zr5bqfrmm3z2a2325jb48spm6ijb5903wry", "depends": ["EBarrays", "mclust", "minqa"] }, "EDASeq": { "name": "EDASeq", "version": "2.42.0", "sha256": "0ij2aa4a5x4s636lx3sc9f81r97x4dl17dnigf632zmkiy84h3i5", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocManager", "Biostrings", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "ShortRead", "aroma_light", "biomaRt"] }, "EDIRquery": { "name": "EDIRquery", "version": "1.8.0", "sha256": "1lrlh5vkgxxbx0yy82fszjf4c9lqz7f9in1xib3ndnhn87jz52k8", "depends": ["GenomicRanges", "InteractionSet", "readr", "tibble", "tictoc"] }, "EGAD": { "name": "EGAD", "version": "1.36.0", "sha256": "0jhsal57sfa9f8c0sxj2vg2y8i3djl84i0qcczd6zrfg22jlpnfz", "depends": ["Biobase", "GEOquery", "MASS", "RColorBrewer", "RCurl", "gplots", "igraph", "impute", "limma", "plyr", "zoo"] }, "EGSEA": { "name": "EGSEA", "version": "1.36.0", "sha256": "0ria6saf1ki2pip4l1r7f4lhzxjfb4pk1791xxc7v0pwmz31ar70", "depends": ["AnnotationDbi", "Biobase", "DT", "EGSEAdata", "GSVA", "HTMLUtils", "PADOG", "RColorBrewer", "edgeR", "gage", "ggplot2", "globaltest", "gplots", "htmlwidgets", "hwriter", "limma", "metap", "org_Hs_eg_db", "org_Mm_eg_db", "org_Rn_eg_db", "pathview", "plotly", "safe", "stringi", "topGO"] }, "ELMER": { "name": "ELMER", "version": "2.32.0", "sha256": "06nyap0qalkycvj7z4bx2d3ii694rdc7cdv498xingxln54b25d7", "depends": ["ComplexHeatmap", "DelayedArray", "ELMER_data", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "Matrix", "MultiAssayExperiment", "S4Vectors", "SummarizedExperiment", "TCGAbiolinks", "biomaRt", "circlize", "doParallel", "downloader", "dplyr", "ggplot2", "ggpubr", "ggrepel", "gridExtra", "lattice", "magrittr", "plotly", "plyr", "progress", "purrr", "readr", "reshape", "reshape2", "rmarkdown", "rtracklayer", "rvest", "scales", "stringr", "tibble", "tidyr", "xml2"] }, "ELViS": { "name": "ELViS", "version": "1.0.0", "sha256": "0xxdrp51mlk4vn317wm01nximzwvdg47gvy6rwbr4ivnr5m7s89k", "depends": ["BiocGenerics", "ComplexHeatmap", "GenomicFeatures", "GenomicRanges", "IRanges", "basilisk", "circlize", "data_table", "dplyr", "ggplot2", "glue", "igraph", "magrittr", "memoise", "patchwork", "scales", "segclust2d", "stringr", "txdbmaker", "uuid", "zoo"] }, "EMDomics": { "name": "EMDomics", "version": "2.38.0", "sha256": "0xg8kpsf2lrjw94lh3m0s7k6092mmfvkc1r4ylikkzspq1yk857h", "depends": ["BiocParallel", "CDFt", "emdist", "ggplot2", "matrixStats", "preprocessCore"] }, "ENmix": { "name": "ENmix", "version": "1.44.3", "sha256": "0xlf0661gam69ajvy74bg09fmlm9mqq0sb4vbp0ag9lpk1wr3yzi", "depends": ["AnnotationHub", "Biobase", "ExperimentHub", "GenomeInfoDb", "IRanges", "RPMM", "S4Vectors", "SummarizedExperiment", "doParallel", "dynamicTreeCut", "foreach", "genefilter", "geneplotter", "gplots", "gtools", "illuminaio", "impute", "irlba", "matrixStats", "minfi", "quadprog"] }, "ERSSA": { "name": "ERSSA", "version": "1.26.0", "sha256": "0x0r1kv1x91lxgczzf57qz8vxpvn6vflgm0v2cn2r6w9q3ydk23j", "depends": ["BiocParallel", "DESeq2", "RColorBrewer", "apeglm", "edgeR", "ggplot2", "plyr"] }, "EWCE": { "name": "EWCE", "version": "1.16.0", "sha256": "0ibbj6m344mf5n1wk9l8xgpczvkjmbiysmlf58f41la25r2nja5x", "depends": ["BiocParallel", "DelayedArray", "HGNChelper", "Matrix", "RNOmni", "SingleCellExperiment", "SummarizedExperiment", "data_table", "dplyr", "ewceData", "ggplot2", "limma", "orthogene", "reshape2", "stringr"] }, "EasyCellType": { "name": "EasyCellType", "version": "1.10.0", "sha256": "0360xqgcrhx7hcw3afam7y83s3wgzl53fnyjpv22rsyll0nx7vdx", "depends": ["AnnotationDbi", "BiocStyle", "clusterProfiler", "dplyr", "forcats", "ggplot2", "magrittr", "org_Hs_eg_db", "org_Mm_eg_db", "rlang", "vctrs"] }, "EmpiricalBrownsMethod": { "name": "EmpiricalBrownsMethod", "version": "1.36.0", "sha256": "139nj1iafr79psi6qpy32lw08whrphcqj621wf7j66lfb7l9kvh0", "depends": [] }, "EnMCB": { "name": "EnMCB", "version": "1.20.0", "sha256": "1m3sbmlcq8441mqyh9dz27qb2wi0hp2jyzgswa6ca7y7m56g3ski", "depends": ["BiocFileCache", "Matrix", "boot", "e1071", "ggplot2", "glmnet", "igraph", "mboost", "rms", "survival", "survivalROC", "survivalsvm"] }, "EnhancedVolcano": { "name": "EnhancedVolcano", "version": "1.26.0", "sha256": "19dxqk5dk9443a3949y3b2dhcphhn2lvi6fvlakqxll2lvhjqivi", "depends": ["ggplot2", "ggrepel"] }, "EnrichDO": { "name": "EnrichDO", "version": "1.2.0", "sha256": "1qk9jw0nb0xgy346p69p4b15ax9kcpfbc1axk1hw92zdxhczpxpn", "depends": ["BiocGenerics", "Rgraphviz", "S4Vectors", "clusterProfiler", "dplyr", "ggplot2", "graph", "hash", "magrittr", "pheatmap", "purrr", "tidyr"] }, "EnrichedHeatmap": { "name": "EnrichedHeatmap", "version": "1.38.0", "sha256": "1l1rpbwd0l48rfgs6y4bk922h0ihyb8ds1ch6ckznwmis48pnlca", "depends": ["ComplexHeatmap", "GenomicRanges", "GetoptLong", "IRanges", "Rcpp", "circlize", "locfit", "matrixStats"] }, "EnrichmentBrowser": { "name": "EnrichmentBrowser", "version": "2.38.0", "sha256": "0z7yc1r41jikbhb3x2pgzhq7c3my0r9i9001wdvdsxpsxas11f4x", "depends": ["AnnotationDbi", "BiocFileCache", "BiocManager", "GO_db", "GSEABase", "KEGGREST", "KEGGgraph", "Rgraphviz", "S4Vectors", "SPIA", "SummarizedExperiment", "edgeR", "graph", "graphite", "hwriter", "limma", "pathview", "safe"] }, "EpiCompare": { "name": "EpiCompare", "version": "1.12.0", "sha256": "1yd56d40lv4wpdd1gw9cs3ds50q3fzyhn09qvwp1x8dr1df7khrf", "depends": ["AnnotationHub", "BiocGenerics", "ChIPseeker", "GenomeInfoDb", "GenomicRanges", "IRanges", "data_table", "downloadthis", "genomation", "ggplot2", "htmltools", "plotly", "reshape2", "rmarkdown", "rtracklayer", "stringr"] }, "EpiDISH": { "name": "EpiDISH", "version": "2.24.0", "sha256": "1jq1vk4g3fij7yanap17xwvk7wrypgj11axbv7chg7m7m66r3p5a", "depends": ["MASS", "Matrix", "e1071", "locfdr", "matrixStats", "quadprog", "stringr"] }, "EpiMix": { "name": "EpiMix", "version": "1.10.0", "sha256": "10s6nqrnpyx0w799iddgl01snk4cl94j5glhydyclxn6893i68dm", "depends": ["AnnotationDbi", "AnnotationHub", "Biobase", "ELMER_data", "EpiMix_data", "ExperimentHub", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RColorBrewer", "RCurl", "RPMM", "R_matlab", "S4Vectors", "SummarizedExperiment", "biomaRt", "data_table", "doParallel", "doSNOW", "downloader", "dplyr", "foreach", "ggplot2", "impute", "limma", "plyr", "progress", "rlang", "tibble", "tidyr"] }, "EpiTxDb": { "name": "EpiTxDb", "version": "1.20.0", "sha256": "1i0bkwpqi9ffnb31c7nkc1046x45kr7zrrkhg2bnvwm080bpzl0z", "depends": ["AnnotationDbi", "BiocFileCache", "BiocGenerics", "Biostrings", "DBI", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Modstrings", "RSQLite", "S4Vectors", "curl", "httr", "rex", "tRNAdbImport", "txdbmaker", "xml2"] }, "EpipwR": { "name": "EpipwR", "version": "1.2.0", "sha256": "1zk4khh0pi3vqkq3k7z9zkimaigzssd1v6ymlqncq9qyrqbyn8kx", "depends": ["EpipwR_data", "ExperimentHub", "ggplot2"] }, "EventPointer": { "name": "EventPointer", "version": "3.16.0", "sha256": "0kli48ckmirifqgrb15nbpyjfd7zlmprpnwkiqncwxcfd8sp5ask", "depends": ["BSgenome", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "MASS", "Matrix", "RBGL", "S4Vectors", "SGSeq", "SummarizedExperiment", "abind", "affxparser", "cobs", "doParallel", "fgsea", "foreach", "glmnet", "graph", "igraph", "iterators", "limma", "lpSolve", "matrixStats", "nnls", "poibin", "prodlim", "qvalue", "rhdf5", "speedglm", "stringr", "tximport"] }, "ExCluster": { "name": "ExCluster", "version": "1.26.0", "sha256": "12x3l7vav6xwc7gmmp9bpl7xjnsd33hxyr70ilhl4j9a3f9609l7", "depends": ["GenomicRanges", "IRanges", "Rsubread", "matrixStats", "rtracklayer"] }, "ExiMiR": { "name": "ExiMiR", "version": "2.50.0", "sha256": "1gki46ajd8xmhxiqs23wz7xxq96q1srafgzvi7snf2dbkaca9xnc", "depends": ["Biobase", "affy", "affyio", "limma", "preprocessCore"] }, "ExperimentHub": { "name": "ExperimentHub", "version": "2.16.1", "sha256": "1pgd1ai6l84y5f7s3mq58g3mpafczakm6aclzl8zi5d7yxqkd2cm", "depends": ["AnnotationHub", "BiocFileCache", "BiocGenerics", "BiocManager", "S4Vectors", "rappdirs"] }, "ExperimentHubData": { "name": "ExperimentHubData", "version": "1.34.0", "sha256": "19n37gf7kz8jvm90f1lg0mc7izvbdy9wasp59qq3l89gifvj3ky6", "depends": ["AnnotationHubData", "BiocGenerics", "BiocManager", "DBI", "ExperimentHub", "S4Vectors", "curl", "httr"] }, "ExperimentSubset": { "name": "ExperimentSubset", "version": "1.18.1", "sha256": "0hmdjg7i6j53f3wna8khd9h9vn23kp521s0c5370yqcjv03a6lbm", "depends": ["Matrix", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "TreeSummarizedExperiment"] }, "ExploreModelMatrix": { "name": "ExploreModelMatrix", "version": "1.20.0", "sha256": "0zm0kjx6ckxldq76yaac26s9bm398xk8fqan9p0jwsapp729l085", "depends": ["DT", "MASS", "S4Vectors", "cowplot", "dplyr", "ggplot2", "limma", "magrittr", "rintrojs", "scales", "shiny", "shinydashboard", "shinyjs", "tibble", "tidyr"] }, "ExpressionAtlas": { "name": "ExpressionAtlas", "version": "2.0.0", "sha256": "0hwy4w7p8afx0jgi1sdczb6qcffpyjmj5rap432zb8fra1wmrdv7", "depends": ["Biobase", "BiocStyle", "RCurl", "S4Vectors", "SummarizedExperiment", "XML", "httr", "jsonlite", "limma", "xml2"] }, "FEAST": { "name": "FEAST", "version": "1.16.0", "sha256": "01490rmdb8xpcpa0l62r8b1v5i4blpgiljwnndzgardwsi1ylxzm", "depends": ["BiocParallel", "SC3", "SingleCellExperiment", "SummarizedExperiment", "TSCAN", "irlba", "matrixStats", "mclust"] }, "FELLA": { "name": "FELLA", "version": "1.28.0", "sha256": "1l7rbp02z7w4vl80ablrdvp689i54lm1l35wjgqlmiijxh9f81il", "depends": ["KEGGREST", "Matrix", "igraph", "plyr"] }, "FGNet": { "name": "FGNet", "version": "3.42.0", "sha256": "0z7zpwk6fcbxi0lxmxl2hlfx7p7hwxjqiwz3lyq6z3cwa10fhk0a", "depends": ["RColorBrewer", "R_utils", "XML", "hwriter", "igraph", "plotrix", "png", "reshape2"] }, "FISHalyseR": { "name": "FISHalyseR", "version": "1.42.0", "sha256": "1z5zypnbkfba1l81wxy4z39m8q8qj03254x458l86nx2xcl45y6w", "depends": ["EBImage", "abind"] }, "FLAMES": { "name": "FLAMES", "version": "2.2.0", "sha256": "0h3lxrdacmch21lpf91alnmjsnca9l4r80r093rvzqagrm002ji5", "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "ComplexHeatmap", "DropletUtils", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "MatrixGenerics", "RColorBrewer", "Rcpp", "Rhtslib", "Rsamtools", "S4Vectors", "SingleCellExperiment", "SparseArray", "SpatialExperiment", "SummarizedExperiment", "abind", "bambu", "basilisk", "circlize", "cowplot", "dplyr", "future", "ggbio", "ggplot2", "gridExtra", "igraph", "jsonlite", "magick", "magrittr", "readr", "reticulate", "rtracklayer", "scater", "scatterpie", "scran", "scuttle", "stringr", "testthat", "tibble", "tidyr", "tidyselect", "txdbmaker", "withr"] }, "FRASER": { "name": "FRASER", "version": "2.4.3", "sha256": "0w7bgfmr72whwnh5nv3bcrk8b4316vds2sgf50qwpcb1v03n066n", "depends": ["AnnotationDbi", "BBmisc", "BSgenome", "Biobase", "BiocGenerics", "BiocParallel", "DelayedArray", "DelayedMatrixStats", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "HDF5Array", "IRanges", "OUTRIDER", "PRROC", "RColorBrewer", "RMTstat", "R_utils", "Rcpp", "RcppArmadillo", "Rsamtools", "Rsubread", "S4Vectors", "SummarizedExperiment", "VGAM", "biomaRt", "cowplot", "data_table", "extraDistr", "generics", "ggplot2", "ggrepel", "matrixStats", "pcaMethods", "pheatmap", "plotly", "pracma", "rhdf5", "tibble"] }, "FRGEpistasis": { "name": "FRGEpistasis", "version": "1.44.0", "sha256": "00y0lvpz2rvpyvv2qb1zwx0iyniivcznrrj9ilr5asspa0pzinkh", "depends": ["MASS", "fda"] }, "FamAgg": { "name": "FamAgg", "version": "1.36.0", "sha256": "0ryhp0yq44p1rcq10f7s3ggkc9h8s8h4qbvx9c2szawagqlfbfp4", "depends": ["BiocGenerics", "Matrix", "gap", "igraph", "kinship2", "survey"] }, "FastqCleaner": { "name": "FastqCleaner", "version": "1.26.0", "sha256": "0slczf0x3vvvfkdpxncf89vplx0vxbhxq042bhfpmxlkd720rhmb", "depends": ["Biostrings", "DT", "IRanges", "Rcpp", "S4Vectors", "ShortRead", "htmltools", "shiny", "shinyBS"] }, "FeatSeekR": { "name": "FeatSeekR", "version": "1.8.0", "sha256": "1yi8gs5vjlqr19a2a2kjiybbf7qaxnzihvhfcrnxr91ajdjrarkb", "depends": ["MASS", "SummarizedExperiment", "pheatmap", "pracma"] }, "FilterFFPE": { "name": "FilterFFPE", "version": "1.18.0", "sha256": "0zc1mm6636kgwx0zw4wxlbw6p7m32smvyphrzfvbf1aff599fjg3", "depends": ["GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "doParallel", "foreach"] }, "FindIT2": { "name": "FindIT2", "version": "1.14.0", "sha256": "0kwckjk0czkvfsr8s2d6rrrkq8vrg36cdxi1laf3qrf7mc9mxwq2", "depends": ["BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "MultiAssayExperiment", "S4Vectors", "SummarizedExperiment", "dplyr", "ggplot2", "ggrepel", "glmnet", "patchwork", "progress", "purrr", "qvalue", "rlang", "rtracklayer", "stringr", "tibble", "tidyr", "withr"] }, "FitHiC": { "name": "FitHiC", "version": "1.34.0", "sha256": "0fkqrj89si23x8dwp4z3fdb6b0zb05578x3jxpsvzvq8bgvpjygm", "depends": ["Rcpp", "data_table", "fdrtool"] }, "FlowSOM": { "name": "FlowSOM", "version": "2.16.0", "sha256": "19x5s09yyxnyk0b4l4mxzx2mq1mqsgcxr7flfazyjcg7qa8kgyld", "depends": ["BiocGenerics", "ConsensusClusterPlus", "Rtsne", "XML", "colorRamps", "dplyr", "flowCore", "ggforce", "ggnewscale", "ggplot2", "ggpubr", "igraph", "magrittr", "rlang", "tidyr"] }, "FuseSOM": { "name": "FuseSOM", "version": "1.10.0", "sha256": "07f6ki9dm268zmwqiimbs12rxzsz00ncvs4hbp6nvn2q0by25pid", "depends": ["FCPS", "Rcpp", "S4Vectors", "SummarizedExperiment", "analogue", "cluster", "coop", "diptest", "fastcluster", "fpc", "ggplot2", "ggplotify", "ggpubr", "pheatmap", "proxy", "psych", "stringr"] }, "G4SNVHunter": { "name": "G4SNVHunter", "version": "1.0.0", "sha256": "1nldzl5rdg1qmayycdkzabivk1aqln8shjksykw5nz2i6vxwhxc7", "depends": ["Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rcpp", "RcppRoll", "S4Vectors", "cowplot", "data_table", "ggplot2", "ggpointdensity", "ggseqlogo", "progress", "viridis"] }, "GA4GHclient": { "name": "GA4GHclient", "version": "1.32.0", "sha256": "0666w3avkkvpah7bkz2qi61wjqn1jjd6xrxz77w6jz0yz42wjlr3", "depends": ["BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "VariantAnnotation", "dplyr", "httr", "jsonlite"] }, "GA4GHshiny": { "name": "GA4GHshiny", "version": "1.30.0", "sha256": "0dnh41pfih21i7pn817zil8sw2jsps7jygzv9w87xfdbikz1chxv", "depends": ["AnnotationDbi", "BiocGenerics", "DT", "GA4GHclient", "GenomeInfoDb", "GenomicFeatures", "S4Vectors", "dplyr", "openxlsx", "purrr", "shiny", "shinyjs", "shinythemes", "tidyr"] }, "GARS": { "name": "GARS", "version": "1.28.0", "sha256": "15izb8wfgn821flbg4wajsz89zd2pa1ydafkx0x93pqjkhl2dik9", "depends": ["DaMiRseq", "MLSeq", "SummarizedExperiment", "cluster", "ggplot2"] }, "GAprediction": { "name": "GAprediction", "version": "1.34.0", "sha256": "1aibsgawv4vgcxwbhyj8c6qjfwpqyck6i7z5l9kpdg9r6ii2bik0", "depends": ["Matrix", "glmnet"] }, "GBScleanR": { "name": "GBScleanR", "version": "2.2.0", "sha256": "1k63l46q8hacq9vg6jpqq23s946p3v1p9ijxkrk29xl8dk02hz19", "depends": ["Rcpp", "RcppParallel", "SeqArray", "expm", "gdsfmt", "ggplot2", "tidyr"] }, "GDCRNATools": { "name": "GDCRNATools", "version": "1.28.0", "sha256": "0aldc1h7zgzqbq8kxfbh3iab8xlyawjxdmm1kajhjmwmiy2w0ya7", "depends": ["BiocParallel", "DESeq2", "DOSE", "DT", "GenomicDataCommons", "XML", "biomaRt", "clusterProfiler", "edgeR", "ggplot2", "gplots", "jsonlite", "limma", "org_Hs_eg_db", "pathview", "rjson", "shiny", "survival", "survminer"] }, "GDSArray": { "name": "GDSArray", "version": "1.28.0", "sha256": "0djk1kj98vj3kgzjk9dcvhx51p804a6v5nl54pxqhlwwm0r3yzgj", "depends": ["BiocGenerics", "DelayedArray", "S4Vectors", "SNPRelate", "SeqArray", "gdsfmt"] }, "GEM": { "name": "GEM", "version": "1.34.0", "sha256": "163yfacdzjklkzfmi1xqc5wwrbwfa8m74s4xrrvv854ri2qsal37", "depends": ["ggplot2"] }, "GENESIS": { "name": "GENESIS", "version": "2.38.0", "sha256": "03nzp87cn8kr01lv1lrai2cbsh0ci611hjk3483rlh6iyjizyx6v", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "GWASTools", "GenomicRanges", "IRanges", "Matrix", "S4Vectors", "SNPRelate", "SeqArray", "SeqVarTools", "data_table", "gdsfmt", "igraph", "reshape2"] }, "GENIE3": { "name": "GENIE3", "version": "1.30.0", "sha256": "1h3nmijn28q7l9y37l32kh42f3gj2fhw7c6ria42yqvqhgcjhj9p", "depends": ["dplyr", "reshape2"] }, "GEOexplorer": { "name": "GEOexplorer", "version": "1.14.0", "sha256": "144pj7aj93rjg315biizapg1m9yywyfx27pk9646klqnrnp2yxi5", "depends": ["Biobase", "DT", "GEOquery", "R_utils", "XML", "car", "edgeR", "enrichR", "factoextra", "ggplot2", "heatmaply", "htmltools", "httr", "impute", "knitr", "limma", "markdown", "pheatmap", "plotly", "readxl", "scales", "shiny", "shinyHeatmaply", "shinybusy", "shinycssloaders", "stringr", "sva", "umap", "xfun", "xml2"] }, "GEOfastq": { "name": "GEOfastq", "version": "1.16.0", "sha256": "1y3jz1zmzpbsfm84pib872n5669w3ggs08dwp2vz1drfz5kh3ldr", "depends": ["RCurl", "doParallel", "foreach", "plyr", "rvest", "stringr", "xml2"] }, "GEOmetadb": { "name": "GEOmetadb", "version": "1.70.0", "sha256": "0vrxg3mj3sspp51hf261jswh3si7vqg8j0ibgfy59il3gn9zjnx0", "depends": ["RSQLite", "R_utils"] }, "GEOquery": { "name": "GEOquery", "version": "2.76.0", "sha256": "17iw6h74qzljcah3m3xzl8hqzmz9v30lafwdbhdfqy8xdhf79jlh", "depends": ["Biobase", "R_utils", "S4Vectors", "SummarizedExperiment", "curl", "data_table", "dplyr", "httr2", "limma", "magrittr", "readr", "rentrez", "rvest", "stringr", "tidyr", "xml2"] }, "GEOsubmission": { "name": "GEOsubmission", "version": "1.60.0", "sha256": "1rc81dq3bm6w09ans7lkk82hmwlkhcs12hi22q0kb5jppllkzff6", "depends": ["Biobase", "affy"] }, "GEWIST": { "name": "GEWIST", "version": "1.52.0", "sha256": "1ylycj5ipdb0k7kf49ki3wd9063ynz5skhj6vnapl3z260ad514f", "depends": ["car"] }, "GGPA": { "name": "GGPA", "version": "1.20.0", "sha256": "0709y2is1a34rq35801mhlmcl869ilsdzdamrbwxn1sbvy2qkzld", "depends": ["GGally", "Rcpp", "RcppArmadillo", "matrixStats", "network", "scales", "sna"] }, "GIGSEA": { "name": "GIGSEA", "version": "1.26.0", "sha256": "02i1fa5k22q39n8a4n07cw5x51qfp33w8zcimplyljpyzr7whi6i", "depends": ["MASS", "Matrix", "locfdr"] }, "GLAD": { "name": "GLAD", "version": "2.72.0", "sha256": "05a1v5b3f6q0ka6sblg56fmcczz5fd80nzvlqcpfg0qd5ck7527h", "depends": ["aws"] }, "GMRP": { "name": "GMRP", "version": "1.36.0", "sha256": "0fz187b5f7xsxgc9l7514dpddm2fi392rdvpc9fp1vbsx7nd6hjn", "depends": ["GenomicRanges", "diagram", "plotrix"] }, "GNET2": { "name": "GNET2", "version": "1.24.0", "sha256": "1w2w2swjakh1cjfwcj1x3y5d3il2am5rxbi3mkxrd48pzwaylync", "depends": ["DiagrammeR", "Rcpp", "SummarizedExperiment", "dplyr", "ggplot2", "igraph", "matrixStats", "reshape2", "xgboost"] }, "GNOSIS": { "name": "GNOSIS", "version": "1.6.0", "sha256": "1q91b8qh0wd587kycbjzs1dlfg33q5yvv34zilz2lfjfkr65q50y", "depends": ["DT", "DescTools", "RColorBrewer", "cBioPortalData", "car", "compareGroups", "dashboardthemes", "fabricatr", "fontawesome", "maftools", "magrittr", "operator_tools", "partykit", "reshape2", "rpart", "rstatix", "shiny", "shinyWidgets", "shinycssloaders", "shinydashboard", "shinydashboardPlus", "shinyjs", "shinylogs", "shinymeta", "survival", "survminer", "tidyverse"] }, "GOSemSim": { "name": "GOSemSim", "version": "2.34.0", "sha256": "1pxz30zfpfwsp9sx3ca99jb5acrsxbl9d7pscm57d767rhm8kq83", "depends": ["AnnotationDbi", "DBI", "GO_db", "R_utils", "Rcpp", "digest", "rlang", "yulab_utils"] }, "GOTHiC": { "name": "GOTHiC", "version": "1.44.0", "sha256": "1ps0v7r0y2abyfk402d2pf5ivnl81hw2fsxz1vrpfywg1al0dy83", "depends": ["BSgenome", "BiocGenerics", "BiocManager", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "ShortRead", "data_table", "ggplot2", "rtracklayer"] }, "GOexpress": { "name": "GOexpress", "version": "1.42.0", "sha256": "02889570wxmpq08lszc072sa7bhv8k8ywgcy0j24xiq8rpww3d70", "depends": ["Biobase", "RColorBrewer", "RCurl", "biomaRt", "ggplot2", "gplots", "randomForest", "stringr"] }, "GOfuncR": { "name": "GOfuncR", "version": "1.28.0", "sha256": "0db0n6c2zz4x8ayxcarxa0gwww5jd2l2pq08q89xil1cy551bipm", "depends": ["AnnotationDbi", "GenomicRanges", "IRanges", "Rcpp", "gtools", "mapplots", "vioplot"] }, "GOpro": { "name": "GOpro", "version": "1.34.0", "sha256": "10rn1izwpra3lk60xw5amfxx5xmc5fm24vm4615fz9xk163kmf56", "depends": ["AnnotationDbi", "BH", "GO_db", "IRanges", "MultiAssayExperiment", "Rcpp", "S4Vectors", "dendextend", "doParallel", "foreach", "org_Hs_eg_db"] }, "GOstats": { "name": "GOstats", "version": "2.74.0", "sha256": "0r7nxmd6lr68c2w1g6y85mx6nzc5ric8qji0nqcqixxcjh27c724", "depends": ["AnnotationDbi", "AnnotationForge", "Biobase", "Category", "GO_db", "RBGL", "Rgraphviz", "annotate", "graph"] }, "GPA": { "name": "GPA", "version": "1.20.0", "sha256": "1bcq2m1zn1nrsxvv28a9l0vwp9y8akaha9qjvizr2m7mwx0d54l2", "depends": ["DT", "Rcpp", "ggplot2", "ggrepel", "plyr", "shiny", "shinyBS", "vegan"] }, "GRENITS": { "name": "GRENITS", "version": "1.60.0", "sha256": "06y861ym21vdsg9r88k4nwy38kl3r4z96slasn3wy8pvw8srjk7c", "depends": ["Rcpp", "RcppArmadillo", "ggplot2", "reshape2"] }, "GRaNIE": { "name": "GRaNIE", "version": "1.12.0", "sha256": "1bn3frs3lhlq0abkip72wb3kvqm9h1y9m9qnn72zrb728nghx1fq", "depends": ["AnnotationHub", "Biostrings", "ComplexHeatmap", "DESeq2", "GenomeInfoDb", "GenomicRanges", "Matrix", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "biomaRt", "checkmate", "circlize", "colorspace", "data_table", "dplyr", "ensembldb", "forcats", "futile_logger", "ggplot2", "gridExtra", "igraph", "limma", "magrittr", "matrixStats", "patchwork", "progress", "readr", "reshape2", "rlang", "scales", "stringr", "tibble", "tidyr", "tidyselect", "topGO", "viridis"] }, "GRmetrics": { "name": "GRmetrics", "version": "1.34.0", "sha256": "12wchdvj2h5lw5nq8fb61wia06wz9iyik6v0662fn0vx5xvrra3z", "depends": ["S4Vectors", "SummarizedExperiment", "drc", "ggplot2", "plotly"] }, "GSALightning": { "name": "GSALightning", "version": "1.36.0", "sha256": "06xv5rsd6blxgajndhwh8kb28sp1aq1b0fai4x74rpfkmvlrf2r5", "depends": ["Matrix", "data_table"] }, "GSAR": { "name": "GSAR", "version": "1.42.0", "sha256": "1a5bfinak614x057kaacn74vff3f9cy2m715w4kl1i6y8x1d1w0a", "depends": ["igraph"] }, "GSCA": { "name": "GSCA", "version": "2.38.0", "sha256": "1ydwjnpw1ckj60gixymak1rv4j8ri7ms0dyrxns78vmpbl4zdm2d", "depends": ["RColorBrewer", "ggplot2", "gplots", "reshape2", "rhdf5", "shiny", "sp"] }, "GSEABase": { "name": "GSEABase", "version": "1.70.0", "sha256": "122akpdafm4kpbcjn4bnpfjr48rnmj2jmjrxzv184dp1gwdgqqw5", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "XML", "annotate", "graph"] }, "GSEABenchmarkeR": { "name": "GSEABenchmarkeR", "version": "1.28.1", "sha256": "1hivzp0aisybr64r9yn1wsgr19fpv40fzkw9p3h3mn48yygkyg2c", "depends": ["AnnotationDbi", "AnnotationHub", "Biobase", "BiocFileCache", "BiocParallel", "EnrichmentBrowser", "ExperimentHub", "KEGGandMetacoreDzPathwaysGEO", "KEGGdzPathwaysGEO", "S4Vectors", "SummarizedExperiment", "edgeR"] }, "GSEAlm": { "name": "GSEAlm", "version": "1.68.0", "sha256": "0i9bpir41ml2bd8wpl1ldv5syjg788zy7hmvdd9yd82fjlflpfxi", "depends": ["Biobase"] }, "GSEAmining": { "name": "GSEAmining", "version": "1.18.0", "sha256": "119n5nqlq5700xzljv7jfiganw70cvzcpn2aw6831da2d3wlyv0j", "depends": ["dendextend", "dplyr", "ggplot2", "ggwordcloud", "gridExtra", "rlang", "stringr", "tibble", "tidytext"] }, "GSRI": { "name": "GSRI", "version": "2.56.0", "sha256": "121pxkb1k8z8lzj5rxh24n26v8427vw7mfgqn20s52pss8rh2p9r", "depends": ["Biobase", "GSEABase", "fdrtool", "genefilter", "les"] }, "GSReg": { "name": "GSReg", "version": "1.42.0", "sha256": "1vnxhclwfdmf53xjkq4iw3wvgnm37x28c1pz23qcp49kl5k7k5gz", "depends": ["AnnotationDbi", "GenomicFeatures", "Homo_sapiens", "org_Hs_eg_db"] }, "GSVA": { "name": "GSVA", "version": "2.2.0", "sha256": "0xnn5v9p2rvy7z935ni8a7psxdl07mzw44sdi63n33rgj8kcnlax", "depends": ["Biobase", "BiocParallel", "BiocSingular", "DelayedArray", "DelayedMatrixStats", "GSEABase", "HDF5Array", "IRanges", "Matrix", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "cli", "sparseMatrixStats"] }, "GSgalgoR": { "name": "GSgalgoR", "version": "1.18.0", "sha256": "0sf6jrcbzl2pm5iviy4vxgp2zw6923b7gx85r20475wgq71wgdb2", "depends": ["cluster", "doParallel", "foreach", "matchingR", "nsga2R", "proxy", "survival"] }, "GUIDEseq": { "name": "GUIDEseq", "version": "1.38.0", "sha256": "18r2i6d7gak1w065a2xjd5hn7viaqdl2q7vcipgfzakqsbhczgxi", "depends": ["BSgenome", "BiocGenerics", "Biostrings", "CRISPRseek", "ChIPpeakAnno", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "data_table", "dplyr", "ggplot2", "hash", "limma", "matrixStats", "multtest", "openxlsx", "patchwork", "purrr", "pwalign", "rio", "rlang", "stringr", "tidyr"] }, "GWAS_BAYES": { "name": "GWAS.BAYES", "version": "1.18.0", "sha256": "1mh606v8ajc8zp5dhxhrxvbs8101mkdy3caxhh8p0br3vwland9c", "depends": ["GA", "MASS", "Matrix", "caret", "limma", "memoise"] }, "GWASTools": { "name": "GWASTools", "version": "1.54.0", "sha256": "0b2jgaald2b1m2gz2s54ar0kyk0bbn6f50h9i13g2phpfanv3j1k", "depends": ["Biobase", "DBI", "DNAcopy", "GWASExactHW", "RSQLite", "data_table", "gdsfmt", "lmtest", "logistf", "quantsmooth", "sandwich", "survival"] }, "GWENA": { "name": "GWENA", "version": "1.18.0", "sha256": "13w9989ama92k2ds2apsyb6dbs5w09p34vhiy5mkayqsr2s3l2wn", "depends": ["NetRep", "RColorBrewer", "SummarizedExperiment", "WGCNA", "cluster", "dplyr", "dynamicTreeCut", "ggplot2", "gprofiler2", "igraph", "magrittr", "matrixStats", "purrr", "rlist", "stringr", "tibble", "tidyr"] }, "GateFinder": { "name": "GateFinder", "version": "1.28.0", "sha256": "1rcqpv33y2n4k96id2r2g59wix9rc06byn7c0rb1kq3nmhgzr4vh", "depends": ["diptest", "flowCore", "flowFP", "mvoutlier", "splancs"] }, "GeDi": { "name": "GeDi", "version": "1.4.0", "sha256": "0mxnbk0xqwc8v4vn50s59gb8gxl5y4dwy8n6sg2ydd23qzd2al9p", "depends": ["BiocFileCache", "BiocNeighbors", "BiocParallel", "ComplexHeatmap", "DT", "GOSemSim", "GeneTonic", "Matrix", "RColorBrewer", "STRINGdb", "bs4Dash", "circlize", "cluster", "dplyr", "fontawesome", "ggdendro", "ggplot2", "igraph", "plotly", "readxl", "rintrojs", "scales", "shiny", "shinyBS", "shinyWidgets", "shinycssloaders", "tm", "visNetwork", "wordcloud2"] }, "GenProSeq": { "name": "GenProSeq", "version": "1.12.0", "sha256": "0izkzms0xlb2pvhc766lyhc0lw1z889k49060xs4bk9kf4saw1yj", "depends": ["CatEncoders", "DeepPINCS", "keras", "mclust", "reticulate", "tensorflow", "ttgsea", "word2vec"] }, "GenVisR": { "name": "GenVisR", "version": "1.39.0", "sha256": "1ax1r53zdjgmgfkj6y9hfd6w19wprpsm6mfbpi168cdskivnpva3", "depends": ["AnnotationDbi", "BSgenome", "BiocGenerics", "Biostrings", "DBI", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "VariantAnnotation", "biomaRt", "data_table", "ggplot2", "gridExtra", "gtable", "gtools", "plyr", "reshape2", "scales", "viridis"] }, "GeneBreak": { "name": "GeneBreak", "version": "1.38.0", "sha256": "0k5pg20qmhzbmjpl8ncarrygqm6g49m1z8hpx42zcqpkmmhw3zc3", "depends": ["CGHbase", "CGHcall", "GenomicRanges", "QDNAseq"] }, "GeneExpressionSignature": { "name": "GeneExpressionSignature", "version": "1.54.0", "sha256": "18n2is10v2x9s8yjv5z7q3ban4jkvz623w343ilnzc7il2nkiaxc", "depends": ["Biobase"] }, "GeneGA": { "name": "GeneGA", "version": "1.58.0", "sha256": "0cnjgvxp7liimbc6axm565521jqc4srkbk9xf5269hw9i60p8370", "depends": ["hash", "seqinr"] }, "GeneGeneInteR": { "name": "GeneGeneInteR", "version": "1.33.0", "sha256": "1wsm0l14mx2qd9gcs6m2n2pn0sgymf79fm8kvxjxvijqjv8n82ca", "depends": ["FactoMineR", "GenomicRanges", "IRanges", "Rsamtools", "data_table", "igraph", "kernlab", "mvtnorm", "snpStats"] }, "GeneMeta": { "name": "GeneMeta", "version": "1.80.0", "sha256": "1wsiqhjz94lfj766v4qafgnqv691vsd9kawxids7g8133fd02ksc", "depends": ["Biobase", "genefilter"] }, "GeneNetworkBuilder": { "name": "GeneNetworkBuilder", "version": "1.50.0", "sha256": "14f4cb5w7ymlvcl3b61nhbnrl0f2q9l37fhlgchxh2ps397mxada", "depends": ["RCy3", "Rcpp", "Rgraphviz", "XML", "graph", "htmlwidgets", "plyr", "rjson"] }, "GeneOverlap": { "name": "GeneOverlap", "version": "1.44.0", "sha256": "0fb380czwrnb7s8my1vdzpj3vakjvclqhvbwr0ycnlhc74n2n3np", "depends": ["RColorBrewer", "gplots"] }, "GeneRegionScan": { "name": "GeneRegionScan", "version": "1.64.0", "sha256": "1zfimj9xdvwn49ijzhpfncic3kqxpdyg5pvwiwy5v0179ymdc86z", "depends": ["Biobase", "Biostrings", "RColorBrewer", "S4Vectors", "affxparser"] }, "GeneSelectMMD": { "name": "GeneSelectMMD", "version": "2.52.0", "sha256": "0khxl4zlkm8rap01k3sdfm7q61pby4fsrh6scxcjndjrkf5ap6q5", "depends": ["Biobase", "MASS", "limma"] }, "GeneStructureTools": { "name": "GeneStructureTools", "version": "1.28.0", "sha256": "1rrlsfyvcni5b8ybbavkvf8pk2m0690irynl7jlvp5i2igfia3ll", "depends": ["BSgenome_Mmusculus_UCSC_mm10", "Biostrings", "GenomicRanges", "Gviz", "IRanges", "S4Vectors", "data_table", "plyr", "rtracklayer", "stringdist", "stringr"] }, "GeneTonic": { "name": "GeneTonic", "version": "3.2.0", "sha256": "1q61akm9sllrjbk3dy2mbvcv0fl10qyqvgvwaz1klixkfwi03hm3", "depends": ["AnnotationDbi", "ComplexHeatmap", "ComplexUpset", "DESeq2", "DT", "GO_db", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "backbone", "bs4Dash", "circlize", "colorspace", "colourpicker", "dendextend", "dplyr", "dynamicTreeCut", "expm", "ggforce", "ggplot2", "ggrepel", "ggridges", "igraph", "matrixStats", "mosdef", "plotly", "rintrojs", "rlang", "rmarkdown", "scales", "shiny", "shinyAce", "shinyWidgets", "shinycssloaders", "tidyr", "tippy", "viridis", "visNetwork"] }, "GeneticsPed": { "name": "GeneticsPed", "version": "1.70.0", "sha256": "01ikcv8qxfwnffs8mqvis68c91xqbshkzpaqz5as810i7vkvqkln", "depends": ["MASS", "gdata", "genetics"] }, "GenomAutomorphism": { "name": "GenomAutomorphism", "version": "1.10.0", "sha256": "1wnwxzpzy4h4vi1dhqqx67q5bn8fwl0h48g4b59sipwd8s0w4v5d", "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "XVector", "data_table", "doParallel", "dplyr", "foreach", "matrixStats", "numbers"] }, "GenomeInfoDb": { "name": "GenomeInfoDb", "version": "1.44.1", "sha256": "1vws4pal7hjq100v7z6xdrvwayk8ry0h7v0jnahhdib3dcs3nl6w", "depends": ["BiocGenerics", "GenomeInfoDbData", "IRanges", "S4Vectors", "UCSC_utils"] }, "GenomicAlignments": { "name": "GenomicAlignments", "version": "1.44.0", "sha256": "048j2jr1jpgjckl18wx35q518ydv8b2bmdiyiaxjc65283b77614", "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "SummarizedExperiment"] }, "GenomicDataCommons": { "name": "GenomicDataCommons", "version": "1.32.1", "sha256": "186z5mph396yj7wv0a5whcxdw3p9mqsyhl7r1wqdcdgvvfx72mys", "depends": ["GenomicRanges", "IRanges", "dplyr", "httr", "jsonlite", "rappdirs", "readr", "rlang", "tibble", "tidyr", "xml2"] }, "GenomicDistributions": { "name": "GenomicDistributions", "version": "1.16.1", "sha256": "0sqbaqnvw3q7mfjqcqaj5bsy59000kxyzvf4jhpl9jwj4ml891ya", "depends": ["Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "broom", "data_table", "dplyr", "ggplot2", "plyr", "reshape2", "scales"] }, "GenomicFeatures": { "name": "GenomicFeatures", "version": "1.60.0", "sha256": "16j78sgjk0hrdbhcbwrwq03355bvgg4d3lzvy773ypg8pwg0jjid", "depends": ["AnnotationDbi", "BiocGenerics", "Biostrings", "DBI", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "XVector", "rtracklayer"] }, "GenomicFiles": { "name": "GenomicFiles", "version": "1.44.1", "sha256": "1k18kjsg15iw3vcpjjd4w04qkv1vfwajbrs0qr2fdxxbwsqq83yn", "depends": ["BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "MatrixGenerics", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "rtracklayer"] }, "GenomicInteractionNodes": { "name": "GenomicInteractionNodes", "version": "1.12.0", "sha256": "0wkzkrd8s8fb7jhpwpl3w97bs4ja0r1xfzcc50ccwynlp4cx4sr2", "depends": ["AnnotationDbi", "GO_db", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RBGL", "S4Vectors", "graph"] }, "GenomicInteractions": { "name": "GenomicInteractions", "version": "1.42.0", "sha256": "02wwbxn9kcpscvkkllad42wa8i5nfqc54nmm550zfhh15qlvazys", "depends": ["Biobase", "BiocGenerics", "GenomeInfoDb", "GenomicRanges", "Gviz", "IRanges", "InteractionSet", "Rsamtools", "S4Vectors", "data_table", "dplyr", "ggplot2", "gridExtra", "igraph", "rtracklayer", "stringr"] }, "GenomicOZone": { "name": "GenomicOZone", "version": "1.22.0", "sha256": "0j2xp2c65l491z753vmpis2a988dq0af0vfhm1m8nbhfd8n45lnd", "depends": ["Ckmeans_1d_dp", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rdpack", "S4Vectors", "biomaRt", "ggbio", "ggplot2", "gridExtra", "lsr", "plyr"] }, "GenomicPlot": { "name": "GenomicPlot", "version": "1.6.1", "sha256": "0fjdnzgwlifdbh3yzlg9mqxbr0l5rg2av41jlwaici1lcjhcq9js", "depends": ["BiocGenerics", "ComplexHeatmap", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "RCAS", "Rsamtools", "VennDiagram", "circlize", "cowplot", "dplyr", "edgeR", "genomation", "ggplot2", "ggplotify", "ggpubr", "ggsci", "ggsignif", "plyranges", "rtracklayer", "scales", "tidyr", "txdbmaker", "viridis"] }, "GenomicRanges": { "name": "GenomicRanges", "version": "1.60.0", "sha256": "082g27miaa13nyjbr6ygc3928kbn5nkmb4l3si4z85dj26k6xgs8", "depends": ["BiocGenerics", "GenomeInfoDb", "IRanges", "S4Vectors", "XVector"] }, "GenomicScores": { "name": "GenomicScores", "version": "2.20.2", "sha256": "0mp0vbbzwry6spjyzizw19r1azccw8ndq48zlppyj02lxspdncgy", "depends": ["AnnotationHub", "Biobase", "BiocFileCache", "BiocGenerics", "BiocManager", "Biostrings", "DelayedArray", "GenomeInfoDb", "GenomicRanges", "HDF5Array", "IRanges", "S4Vectors", "XML", "httr", "rhdf5"] }, "GenomicSuperSignature": { "name": "GenomicSuperSignature", "version": "1.16.1", "sha256": "0mkmzy0ifcqdl74zhkgqymdvm7w7l2hlzga7m11ggcjkr8yiq7pk", "depends": ["Biobase", "BiocFileCache", "ComplexHeatmap", "S4Vectors", "SummarizedExperiment", "dplyr", "flextable", "ggplot2", "ggpubr", "irlba", "plotly"] }, "GenomicTuples": { "name": "GenomicTuples", "version": "1.42.0", "sha256": "1i7rfnq16fl053s9y8dgiyik4g50c69zymx9iarz3haryr945vrj", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rcpp", "S4Vectors", "data_table"] }, "GeoDiff": { "name": "GeoDiff", "version": "1.14.0", "sha256": "0dzlksssdmz4bvscak9x8k7bxkk6lc4xhdljqgdm6fslsbywlbqy", "depends": ["Biobase", "GeomxTools", "Matrix", "NanoStringNCTools", "Rcpp", "RcppArmadillo", "lme4", "plyr", "robust", "roptim", "testthat", "withr"] }, "GeoTcgaData": { "name": "GeoTcgaData", "version": "2.8.0", "sha256": "1yi3dbb6gamnsi2lgfr9rhh981pmhsqmvjlniczxdh1rwdpixrzl", "depends": ["SummarizedExperiment", "cqn", "data_table", "plyr", "topconfects"] }, "GeomxTools": { "name": "GeomxTools", "version": "3.12.0", "sha256": "1v2gslpagchv0j4cgp431i8lbbkk4sfwndwdpxk61da36d83fg3k", "depends": ["Biobase", "BiocGenerics", "EnvStats", "GGally", "NanoStringNCTools", "S4Vectors", "SeuratObject", "data_table", "dplyr", "ggplot2", "lmerTest", "readxl", "reshape2", "rjson", "rlang", "stringr"] }, "GladiaTOX": { "name": "GladiaTOX", "version": "1.24.1", "sha256": "0a5lhxv8n3h6jimvq12qxcb2m6ix1mi23kjgfi2lxnfz1wdma1h4", "depends": ["DBI", "RColorBrewer", "RCurl", "RJSONIO", "RMariaDB", "RSQLite", "XML", "brew", "data_table", "ggplot2", "ggrepel", "numDeriv", "stringr", "tidyr", "xtable"] }, "Glimma": { "name": "Glimma", "version": "2.18.0", "sha256": "1mrx7l7s3ddvlqrzb3wgx3nis1nd4jjfmamdnlcpl09x4x3fd4w2", "depends": ["DESeq2", "S4Vectors", "SummarizedExperiment", "edgeR", "htmlwidgets", "jsonlite", "limma"] }, "GloScope": { "name": "GloScope", "version": "1.6.0", "sha256": "09q9dy0cv2n3f5j31wa9zms4ab7azkivckix6jksqaq5d273fi1n", "depends": ["BiocParallel", "FNN", "MASS", "RANN", "SingleCellExperiment", "ggplot2", "mclust", "mvnfast", "rlang"] }, "GlobalAncova": { "name": "GlobalAncova", "version": "4.26.0", "sha256": "1gmqfchhkz9157g76jl373w7gg5djn83qz5ic0hbgfwlm906xi7a", "depends": ["AnnotationDbi", "Biobase", "GSEABase", "VGAM", "annotate", "corpcor", "dendextend", "globaltest"] }, "GmicR": { "name": "GmicR", "version": "1.22.0", "sha256": "0m3ww2nxp22vjbcy0l66wxr01fmgiz87xqciqs0g9l3yv04iglwa", "depends": ["AnnotationDbi", "Category", "DT", "GOstats", "GSEABase", "WGCNA", "ape", "bnlearn", "data_table", "doParallel", "foreach", "gRain", "gRbase", "org_Hs_eg_db", "org_Mm_eg_db", "reshape2", "shiny"] }, "GrafGen": { "name": "GrafGen", "version": "1.4.0", "sha256": "1bi6d3pyy5spx80chis3gyl3drwhgldb1y5ysv9209mjx24nvqgq", "depends": ["GenomicRanges", "RColorBrewer", "cowplot", "dplyr", "ggplot2", "ggpubr", "plotly", "rlang", "scales", "shiny", "stringr"] }, "GraphAT": { "name": "GraphAT", "version": "1.80.0", "sha256": "1gavp5wplslmxvpk9bjxvvsbb9i5qw3iyny7dypfk4f00gfdd3rl", "depends": ["MCMCpack", "graph"] }, "GraphAlignment": { "name": "GraphAlignment", "version": "1.72.0", "sha256": "0j5f98cz80qy4qzfz5v5fswwbz428a4iv5ph8p3cl8wg7yabz0w7", "depends": [] }, "GreyListChIP": { "name": "GreyListChIP", "version": "1.40.0", "sha256": "1aykzjz3wg82k9ri4vc42dc3s93pjp5raxayq2ysf61v5j8qg17r", "depends": ["BSgenome", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "MASS", "Rsamtools", "SummarizedExperiment", "rtracklayer"] }, "Guitar": { "name": "Guitar", "version": "2.24.0", "sha256": "0nmxfiwfw1q5rn7642k3x1s6p8q7dssm8c0zcqiq6404f5j44qwq", "depends": ["AnnotationDbi", "GenomicFeatures", "GenomicRanges", "dplyr", "ggplot2", "knitr", "magrittr", "rtracklayer"] }, "Gviz": { "name": "Gviz", "version": "1.52.0", "sha256": "1jsvh8mxjsqr9x8nf40jhachk0rf9civ64x34wk3ymn0ym56vj3w", "depends": ["AnnotationDbi", "BSgenome", "Biobase", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "XVector", "biomaRt", "biovizBase", "digest", "ensembldb", "lattice", "latticeExtra", "matrixStats", "rtracklayer"] }, "HDF5Array": { "name": "HDF5Array", "version": "1.36.0", "sha256": "1il3a5vdyf6ddazxqcll1d8ca1bl8q1pq2l5ss9n159isdimb410", "depends": ["BiocGenerics", "DelayedArray", "IRanges", "Matrix", "S4Arrays", "S4Vectors", "SparseArray", "h5mread", "rhdf5"] }, "HDTD": { "name": "HDTD", "version": "1.42.0", "sha256": "0njyi579pvhjxrzrfv8rm74chhblzfd11p2c6nql7qkfw5lj687m", "depends": ["Rcpp", "RcppArmadillo"] }, "HELP": { "name": "HELP", "version": "1.66.0", "sha256": "1r63qfp77mm61yz7iz2hjgfcji028zsrkdxhk88m9w9adchi4fvp", "depends": ["Biobase"] }, "HEM": { "name": "HEM", "version": "1.80.0", "sha256": "12lb81lasxwazczibpydppbn2z64qfkcpbaa08f959i1gridf98b", "depends": ["Biobase"] }, "HERON": { "name": "HERON", "version": "1.6.1", "sha256": "0wcfbvy367jjyjw3qpi08knv2kqz528f6grrnlfgcmnlwzxbdr9j", "depends": ["GenomicRanges", "IRanges", "Matrix", "S4Vectors", "SummarizedExperiment", "cluster", "data_table", "harmonicmeanp", "limma", "matrixStats", "metap", "spdep"] }, "HGC": { "name": "HGC", "version": "1.16.0", "sha256": "0n224nv1ylh79xbd9sdp6283zi3dmia5ng1k51wvkl6hq748m4ba", "depends": ["Matrix", "RANN", "Rcpp", "RcppEigen", "ape", "dendextend", "dplyr", "ggplot2", "mclust", "patchwork"] }, "HIBAG": { "name": "HIBAG", "version": "1.44.0", "sha256": "1yrbw13k0w448q0pg4k8ylik84v9lb5khj7ax2fn4gvmhaa26v7w", "depends": ["RcppParallel"] }, "HIPPO": { "name": "HIPPO", "version": "1.20.0", "sha256": "0k43hcl0byjyi496g73xq8b23mn20m1i0zlfvf1vand6cwrs4zdh", "depends": ["Matrix", "Rtsne", "SingleCellExperiment", "dplyr", "ggplot2", "ggrepel", "gridExtra", "irlba", "magrittr", "reshape2", "rlang", "umap"] }, "HIREewas": { "name": "HIREewas", "version": "1.26.0", "sha256": "105jw39xfm4l7c2ncliba2ismc9xw0chdzkhscd772g9nz20avhs", "depends": ["gplots", "quadprog"] }, "HMMcopy": { "name": "HMMcopy", "version": "1.50.0", "sha256": "1pwhakhx880815dr5gs2m9f4jr402p8h2ccs01n8cbjkm32w6nq7", "depends": ["data_table"] }, "HPAanalyze": { "name": "HPAanalyze", "version": "1.26.1", "sha256": "0lsrk41g8hfpk4jrm6wyl41wlk5pkiy5vr5gcn3zdqn7zg133v28", "depends": ["dplyr", "ggplot2", "gridExtra", "openxlsx", "tibble", "xml2"] }, "HPiP": { "name": "HPiP", "version": "1.14.0", "sha256": "0dbpzacyhwv0080ql3p3gsrmclb5sil9rj3kh2lf7b61qsikh701", "depends": ["MCL", "PRROC", "caret", "corrplot", "dplyr", "ggplot2", "httr", "igraph", "magrittr", "pROC", "protr", "purrr", "readr", "stringr", "tibble", "tidyr"] }, "HTSFilter": { "name": "HTSFilter", "version": "1.48.0", "sha256": "16k9rhbhm24almk2sclsn4w3rp681pmv171y8w8w65mcrl9x3hm9", "depends": ["Biobase", "BiocParallel", "DESeq2", "edgeR"] }, "HTqPCR": { "name": "HTqPCR", "version": "1.62.0", "sha256": "1bky9ybsjj0y9qf3klbdmic8izbqc391p6nz8jk9hjgx54w8xg6g", "depends": ["Biobase", "RColorBrewer", "affy", "gplots", "limma"] }, "Harman": { "name": "Harman", "version": "1.36.0", "sha256": "0j99mi8mxrpmm2ypakc7k9ja59iqsxdn8189a70wipyzs5srnnp5", "depends": ["Ckmeans_1d_dp", "Rcpp", "matrixStats"] }, "HarmonizR": { "name": "HarmonizR", "version": "1.6.0", "sha256": "016bkk6h9w430dpg1afnfwaiy4piz6qyyq26lwng2w0jpvyxr7h9", "depends": ["SummarizedExperiment", "doParallel", "foreach", "janitor", "limma", "plyr", "seriation", "sva"] }, "Harshlight": { "name": "Harshlight", "version": "1.79.0", "sha256": "1jm0ia06ls1m7dsbzp1hk68qi5wbqzhcf6x66534bj1kxdll17k7", "depends": ["Biobase", "affy", "altcdfenvs"] }, "Heatplus": { "name": "Heatplus", "version": "3.16.0", "sha256": "1an32ghqbd2j39509v1anzp65ahndwi6nhjzcvvv5ixl6s006n9k", "depends": ["RColorBrewer"] }, "HelloRanges": { "name": "HelloRanges", "version": "1.34.0", "sha256": "1ihjcwrxsbfd0sv9fdk21vszi9wjw61fycqjxv276a7i1s9r0k37", "depends": ["BSgenome", "BiocGenerics", "BiocIO", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "docopt", "rtracklayer"] }, "Herper": { "name": "Herper", "version": "1.18.0", "sha256": "1x4f11rrnf9sy496w2m94jrrs1ljidkswwyr645h3dcd6rf6igks", "depends": ["reticulate", "rjson", "withr"] }, "HiCBricks": { "name": "HiCBricks", "version": "1.26.0", "sha256": "0gn9n0rgppkwxj4l90aqvaw93mvxaqjfi5h8z52n9azcdb5n91ky", "depends": ["BiocParallel", "GenomeInfoDb", "GenomicRanges", "IRanges", "R6", "RColorBrewer", "R_utils", "S4Vectors", "curl", "data_table", "digest", "ggplot2", "jsonlite", "readr", "reshape2", "rhdf5", "scales", "stringr", "tibble", "viridis"] }, "HiCDCPlus": { "name": "HiCDCPlus", "version": "1.16.0", "sha256": "1r4y5jn56f02bhxamsrimhrp6mk1gk51xnf6jpgi4g3mpli66yv7", "depends": ["BSgenome", "Biostrings", "GenomeInfoDb", "GenomicInteractions", "GenomicRanges", "IRanges", "InteractionSet", "MASS", "R_utils", "Rcpp", "S4Vectors", "bbmle", "data_table", "dplyr", "pscl", "rlang", "rtracklayer", "tibble", "tidyr"] }, "HiCDOC": { "name": "HiCDOC", "version": "1.10.2", "sha256": "056i8q3fblmymlm7qdmijkdwc2gi278bb6pmh07sl2880iw7iwix", "depends": ["BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicRanges", "InteractionSet", "Rcpp", "S4Vectors", "SummarizedExperiment", "cowplot", "data_table", "ggplot2", "gridExtra", "gtools", "multiHiCcompare", "pbapply"] }, "HiCExperiment": { "name": "HiCExperiment", "version": "1.8.0", "sha256": "13ccm1d2k6p4lah9bqq2jqnfba1zm2xk6ifkwy6hzrrxyaxav8xm", "depends": ["BiocGenerics", "BiocIO", "BiocParallel", "GenomeInfoDb", "GenomicRanges", "IRanges", "InteractionSet", "Matrix", "S4Vectors", "dplyr", "rhdf5", "strawr", "vroom"] }, "HiCParser": { "name": "HiCParser", "version": "1.0.0", "sha256": "0dq5s8g6p77i1c7gmhzyz86ylqh3r4v77wf5i702cd7d9xzpaz6j", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "InteractionSet", "Rcpp", "S4Vectors", "SummarizedExperiment", "data_table", "gtools", "pbapply"] }, "HiCcompare": { "name": "HiCcompare", "version": "1.30.0", "sha256": "1v886calffi7al5aibyc8xdk68vla2mif5y3awb3s03s3cb16n2v", "depends": ["BiocParallel", "GenomicRanges", "IRanges", "InteractionSet", "KernSmooth", "S4Vectors", "data_table", "dplyr", "ggplot2", "gridExtra", "gtools", "mgcv", "pheatmap", "rhdf5"] }, "HiContacts": { "name": "HiContacts", "version": "1.10.0", "sha256": "1vwyzskp489vclaw43pqc8gwxr81vi4aia2cg0zjazn7wrjyjgzj", "depends": ["BiocGenerics", "BiocIO", "BiocParallel", "GenomeInfoDb", "GenomicRanges", "HiCExperiment", "IRanges", "InteractionSet", "Matrix", "RSpectra", "S4Vectors", "SummarizedExperiment", "dplyr", "ggplot2", "ggrastr", "readr", "scales", "stringr", "tibble", "tidyr"] }, "HiCool": { "name": "HiCool", "version": "1.8.0", "sha256": "0cnzbi4if3cn0lr78yh4a76kn3pv8c332w69s3l9gsqxvjx16kqs", "depends": ["BiocIO", "GenomicRanges", "HiCExperiment", "IRanges", "InteractionSet", "S4Vectors", "basilisk", "dplyr", "plotly", "reticulate", "rmarkdown", "rmdformats", "sessioninfo", "stringr", "vroom"] }, "HiLDA": { "name": "HiLDA", "version": "1.22.0", "sha256": "1zyf3z2p9ln3zxpqqb18zyn4c8yr6jccagc8wfya6yvp42f2h95y", "depends": ["BSgenome_Hsapiens_UCSC_hg19", "BiocGenerics", "Biostrings", "GenomicFeatures", "GenomicRanges", "R2jags", "Rcpp", "S4Vectors", "TxDb_Hsapiens_UCSC_hg19_knownGene", "XVector", "abind", "cowplot", "forcats", "ggplot2", "stringr", "tidyr"] }, "HiTC": { "name": "HiTC", "version": "1.52.0", "sha256": "0y0srz1w6yp9dkk0zyij7lq18413651z7svv9ydfyimr8gqjb2a9", "depends": ["Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "Matrix", "RColorBrewer", "rtracklayer"] }, "HicAggR": { "name": "HicAggR", "version": "1.4.0", "sha256": "1y8s6dp6ilia1gznv4v09xz7lmhg05h7szharapw0jdqszzygvif", "depends": ["BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicRanges", "IRanges", "InteractionSet", "Matrix", "S4Vectors", "checkmate", "data_table", "dplyr", "ggplot2", "gridExtra", "purrr", "reshape", "rhdf5", "rlang", "rtracklayer", "strawr", "stringr", "tibble", "tidyr", "withr"] }, "HilbertCurve": { "name": "HilbertCurve", "version": "2.2.0", "sha256": "08n25ybwmd5dwd8hl13pfnsni7m7l1irpijfryn649sgigg2nx96", "depends": ["GenomicRanges", "IRanges", "Rcpp", "circlize", "png", "polylabelr"] }, "HilbertVis": { "name": "HilbertVis", "version": "1.66.1", "sha256": "0mgj5m062nyh2f29xjmcwjhv5hqhj8138vhik8c8qn1x1wg2ddlj", "depends": ["lattice"] }, "HilbertVisGUI": { "name": "HilbertVisGUI", "version": "1.66.1", "sha256": "0pavdk7szz82vzplw5pk4zch6sq89s6xvzy2q6aq8i1mf6bb3f4i", "depends": ["HilbertVis"] }, "HoloFoodR": { "name": "HoloFoodR", "version": "1.2.0", "sha256": "1siw3q0byd9vw892kg4rv40jp1d9v001gwfiwzlwn4vpni6hqrjg", "depends": ["MultiAssayExperiment", "S4Vectors", "SummarizedExperiment", "TreeSummarizedExperiment", "dplyr", "httr2", "jsonlite"] }, "HuBMAPR": { "name": "HuBMAPR", "version": "1.2.2", "sha256": "1si9l6f029rjwa2jpgf1nmdkn8n1rfvvyhcaj6yrda6pyb0kpq8q", "depends": ["dplyr", "httr2", "purrr", "rjsoncons", "rlang", "stringr", "tibble", "tidyr", "whisker"] }, "HubPub": { "name": "HubPub", "version": "1.16.0", "sha256": "05w075lp72b0njkf13mvsfy2q1c35bljy9srcczd8f9kvh79n73s", "depends": ["BiocManager", "available", "aws_s3", "biocthis", "dplyr", "fs", "usethis"] }, "HybridExpress": { "name": "HybridExpress", "version": "1.4.0", "sha256": "0d0519kb7sjhnfap93mhxlsfi4mah2s21p7g79bdaks419j8s4c2", "depends": ["BiocParallel", "ComplexHeatmap", "DESeq2", "RColorBrewer", "SummarizedExperiment", "ggplot2", "patchwork", "rlang"] }, "HybridMTest": { "name": "HybridMTest", "version": "1.52.0", "sha256": "1qkzh25d79hmpa6fh9binc3bhsw4yd9h6sdbl5gnxl1nn1cm2rzw", "depends": ["Biobase", "MASS", "fdrtool", "survival"] }, "IFAA": { "name": "IFAA", "version": "1.10.0", "sha256": "1hrd5mwbd6bqxvzgsa0g99vr5kzzsgpip08jbysir9dj99w8gr5j", "depends": ["DescTools", "HDCI", "Matrix", "MatrixExtra", "S4Vectors", "SummarizedExperiment", "doParallel", "doRNG", "foreach", "glmnet", "mathjaxr", "parallelly", "stringr"] }, "IHW": { "name": "IHW", "version": "1.36.0", "sha256": "05qwdcx92ryih2919d7rikliwzy0ddsbf02bqfy1vwa4rgzxna1d", "depends": ["BiocGenerics", "fdrtool", "lpsymphony", "slam"] }, "ILoReg": { "name": "ILoReg", "version": "1.18.0", "sha256": "0rpj6hhn3wl818q4sybl9q1yvsrb8fz1rngj1iyn9z1f0g244wq6", "depends": ["DescTools", "LiblineaR", "Matrix", "RSpectra", "Rtsne", "S4Vectors", "SingleCellExperiment", "SparseM", "SummarizedExperiment", "aricode", "cluster", "cowplot", "dendextend", "doRNG", "doSNOW", "dplyr", "fastcluster", "foreach", "ggplot2", "parallelDist", "pheatmap", "plyr", "reshape2", "scales", "umap"] }, "IMAS": { "name": "IMAS", "version": "1.32.0", "sha256": "1b1vy4mdnna15ckmh6n5jqz4bkyq4izm5zij71brg3b21214c0ja", "depends": ["AnnotationDbi", "BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "IVAS", "Matrix", "Rsamtools", "S4Vectors", "doParallel", "foreach", "ggfortify", "ggplot2", "gridExtra", "lattice", "lme4", "survival"] }, "IMMAN": { "name": "IMMAN", "version": "1.28.0", "sha256": "0n1y0ypkxa8bma3jqpds0hx16iyq8i42vaygx690qk5vll5gs6dh", "depends": ["STRINGdb", "igraph", "pwalign", "seqinr"] }, "IMPCdata": { "name": "IMPCdata", "version": "1.44.0", "sha256": "01vslnask0kslb17vxp48pp6wmm3y4lk12hi398r4ggzq6k56z1x", "depends": ["rjson"] }, "INDEED": { "name": "INDEED", "version": "2.22.0", "sha256": "1dp0kdglk0ygnhmlqvfdwvlvzmc600dm22zxbgzpgg2m1qfx1alv", "depends": ["devtools", "glasso", "igraph", "visNetwork"] }, "INPower": { "name": "INPower", "version": "1.44.0", "sha256": "0nadgph0mi9i830cmmlcih30v2xlxj53j8lgbysa9z358adk67cd", "depends": ["mvtnorm"] }, "INSPEcT": { "name": "INSPEcT", "version": "1.38.0", "sha256": "0k67dmifjpy1csbrcyhibsdixppwwil62rczjxggwrqdskpph1zy", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "DESeq2", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "KernSmooth", "Rsamtools", "S4Vectors", "SummarizedExperiment", "TxDb_Mmusculus_UCSC_mm9_knownGene", "deSolve", "pROC", "plgem", "readxl", "rootSolve", "rtracklayer", "shiny"] }, "INTACT": { "name": "INTACT", "version": "1.8.0", "sha256": "1n0chf0y5dkfnz54fy8rkvhchyk28jyqa3hjxj1ib9hk12zy1nzr", "depends": ["SQUAREM", "bdsmatrix", "ggplot2", "numDeriv", "tidyr"] }, "IONiseR": { "name": "IONiseR", "version": "2.32.0", "sha256": "1wbfgvckws9lya62dxys4rj140qjfz5kaxsj5292lq9r69j160rp", "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "ShortRead", "XVector", "bit64", "dplyr", "ggplot2", "magrittr", "rhdf5", "stringr", "tibble", "tidyr"] }, "IPO": { "name": "IPO", "version": "1.34.0", "sha256": "1lg4k3hrhmgvnqj6w0ic2hblmszllms53zn3dh9yxw445yry9c5h", "depends": ["BiocParallel", "CAMERA", "rsm", "xcms"] }, "IRanges": { "name": "IRanges", "version": "2.42.0", "sha256": "1z03nrhn0nk4aam0vdiw4r41b38ds29jzaprg335y70ijgp03fqa", "depends": ["BiocGenerics", "S4Vectors"] }, "ISAnalytics": { "name": "ISAnalytics", "version": "1.18.0", "sha256": "0mwcjxvsnqygpj4z0c5ib2570ryhxwv8qivvjsgdnl8wlk16z8xm", "depends": ["DT", "bslib", "datamods", "dplyr", "forcats", "fs", "ggplot2", "ggrepel", "glue", "lifecycle", "lubridate", "purrr", "readr", "readxl", "rlang", "shiny", "shinyWidgets", "stringr", "tibble", "tidyr"] }, "ISLET": { "name": "ISLET", "version": "1.10.0", "sha256": "128z6c6108jgcindgk8b43kralcpvshnkrqd1jw70ppgrhk0avgg", "depends": ["BiocGenerics", "BiocParallel", "Matrix", "SummarizedExperiment", "abind", "lme4", "nnls", "purrr"] }, "ISoLDE": { "name": "ISoLDE", "version": "1.36.0", "sha256": "00ij2bjm1hyc3rl38bi47ysysgvp087m79bkf7g205r2lbfjv2ks", "depends": [] }, "ITALICS": { "name": "ITALICS", "version": "2.68.0", "sha256": "0hlqsqk6acjrzaqffrivaq4kd6zbr48a89wh1lwqbgxz20pc29dc", "depends": ["DBI", "GLAD", "ITALICSData", "affxparser", "oligo", "oligoClasses", "pd_mapping50k_xba240"] }, "IVAS": { "name": "IVAS", "version": "2.28.0", "sha256": "0xl2q1zd36cc8qf9c9yhlc4nah68crplkp2agkzqhlbr4gx22z8h", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "S4Vectors", "doParallel", "foreach", "ggfortify", "ggplot2", "lme4"] }, "IWTomics": { "name": "IWTomics", "version": "1.32.0", "sha256": "0ls0yb2iam95wq9kdgdl0fsyh541mf2ai584ybg1w1kpbrypjq6p", "depends": ["GenomicRanges", "IRanges", "KernSmooth", "S4Vectors", "fda", "gtable"] }, "Icens": { "name": "Icens", "version": "1.80.0", "sha256": "125n4kd2b7fd4x198y70wyapab32wmxnf877cq1ngr9ryhlnnjl7", "depends": ["survival"] }, "IdeoViz": { "name": "IdeoViz", "version": "1.44.0", "sha256": "16zrlkhhbc9hmq0pg0fl8q6i6snfhizjrbv5yr1psbqm9p2wvjgh", "depends": ["Biobase", "GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "rtracklayer"] }, "IgGeneUsage": { "name": "IgGeneUsage", "version": "1.22.0", "sha256": "1xfmgfxhxzxi061ff1ac6rfm9pm93mrhaw77ml1cqp5bfd5pr5f9", "depends": ["BH", "Rcpp", "RcppEigen", "RcppParallel", "StanHeaders", "SummarizedExperiment", "reshape2", "rstan", "rstantools", "tidyr"] }, "InPAS": { "name": "InPAS", "version": "2.16.0", "sha256": "0q8klqci4sr39ijvahn9z1jsrc0szv1lc5c1nbrrbgcngw7w7kjb", "depends": ["AnnotationDbi", "BSgenome", "Biobase", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RSQLite", "S4Vectors", "batchtools", "cleanUpdTSeq", "depmixS4", "dplyr", "flock", "future", "future_apply", "ggplot2", "limma", "magrittr", "parallelly", "plyranges", "preprocessCore", "readr", "reshape2"] }, "InTAD": { "name": "InTAD", "version": "1.28.0", "sha256": "1mxqhrkd5f7l77n0dw5n305h0vg35izcfg2g3jd5grc140mcv003", "depends": ["Biobase", "BiocGenerics", "GenomicRanges", "IRanges", "MultiAssayExperiment", "S4Vectors", "SummarizedExperiment", "ggplot2", "ggpubr", "mclust", "qvalue", "rtracklayer"] }, "Informeasure": { "name": "Informeasure", "version": "1.18.0", "sha256": "0yx57py6mnv6ndba69crvyig59367qipb7drzlnn227hvyyc1ms5", "depends": ["entropy"] }, "IntEREst": { "name": "IntEREst", "version": "1.32.0", "sha256": "0mpx75idzghpscxsqf1hkpx5n5q99xrmnwzc4kdyxqm0bmg71q3r", "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "DBI", "DESeq2", "DEXSeq", "GenomicAlignments", "GenomicFeatures", "GenomicFiles", "GenomicRanges", "IRanges", "RMariaDB", "Rsamtools", "S4Vectors", "SummarizedExperiment", "edgeR", "seqLogo", "seqinr", "txdbmaker"] }, "InterCellar": { "name": "InterCellar", "version": "2.14.0", "sha256": "0mx7sygw3ixs2d3ixkj5wfkk7yznlp2hdz3rp7dzgii77n2spza4", "depends": ["ComplexHeatmap", "DT", "biomaRt", "circlize", "colorspace", "colourpicker", "config", "data_table", "dendextend", "dplyr", "factoextra", "fmsb", "fs", "ggplot2", "golem", "htmltools", "htmlwidgets", "igraph", "plotly", "plyr", "readxl", "rlang", "scales", "shiny", "shinyFeedback", "shinyFiles", "shinyalert", "shinycssloaders", "shinydashboard", "signal", "tibble", "tidyr", "umap", "visNetwork", "wordcloud2"] }, "InteractionSet": { "name": "InteractionSet", "version": "1.36.1", "sha256": "043xi3rsal22pxdaldskpmxy64s2gzfrcsm3s192dcvkryzmm80z", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "Matrix", "Rcpp", "S4Vectors", "SummarizedExperiment"] }, "InteractiveComplexHeatmap": { "name": "InteractiveComplexHeatmap", "version": "1.16.0", "sha256": "1xzi7x0p9x8him3wd8v1hy2v01hf8a5jpnxj69s27463jy33kqpf", "depends": ["ComplexHeatmap", "GetoptLong", "IRanges", "RColorBrewer", "S4Vectors", "clisymbols", "digest", "fontawesome", "htmltools", "jsonlite", "kableExtra", "shiny", "svglite"] }, "IntramiRExploreR": { "name": "IntramiRExploreR", "version": "1.30.0", "sha256": "0d43lcc4cmcqh7m4ch6731w5cc61qzyf06lwqpldp0klaybb2gs3", "depends": ["FGNet", "igraph", "knitr"] }, "IsoBayes": { "name": "IsoBayes", "version": "1.6.1", "sha256": "18z7jqz342hkxma3l6wmxjl0wqzg5s3c5602slqdb0asa7xf372f", "depends": ["HDInterval", "Rcpp", "RcppArmadillo", "S4Vectors", "SummarizedExperiment", "data_table", "doParallel", "doRNG", "foreach", "ggplot2", "glue", "iterators"] }, "IsoCorrectoR": { "name": "IsoCorrectoR", "version": "1.26.0", "sha256": "129n4cl72dlk9wdjcxz635gfsag839ilgpxalp355s7p9i56fynd", "depends": ["WriteXLS", "dplyr", "magrittr", "pracma", "quadprog", "readr", "readxl", "stringr", "tibble"] }, "IsoCorrectoRGUI": { "name": "IsoCorrectoRGUI", "version": "1.24.0", "sha256": "19r4x578gjc9jx62l12nzprmwz17mm143xfcdlsgfcb9myb8r4dk", "depends": ["IsoCorrectoR", "readxl", "tcltk2"] }, "IsoformSwitchAnalyzeR": { "name": "IsoformSwitchAnalyzeR", "version": "2.8.0", "sha256": "156v2c8d3szhhpfra3jyczpw5wxv1lhfr4kyfzw3v1l965dci75q", "depends": ["BSgenome", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "DBI", "DEXSeq", "GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "RCurl", "S4Vectors", "SummarizedExperiment", "VennDiagram", "XVector", "dplyr", "edgeR", "futile_logger", "ggplot2", "gridExtra", "limma", "magrittr", "pfamAnalyzeR", "plyr", "pwalign", "readr", "reshape2", "rtracklayer", "satuRn", "stringr", "sva", "tibble", "tidyr", "tximeta", "tximport"] }, "KBoost": { "name": "KBoost", "version": "1.16.0", "sha256": "1m352d1azcqsrjjrcz1s7c1bbqsdq8h8ak0p752ja8z6gcqhslf5", "depends": [] }, "KCsmart": { "name": "KCsmart", "version": "2.66.0", "sha256": "1ys7zpj87i21m7yg8afac85qmjrqqdlr6f7hys04zydpqzq3ldcv", "depends": ["BiocGenerics", "KernSmooth", "multtest", "siggenes"] }, "KEGGREST": { "name": "KEGGREST", "version": "1.48.1", "sha256": "0k380w6qb3yal2vyr894kkc64vlqr63214agi112vw888v71g6in", "depends": ["Biostrings", "httr", "png"] }, "KEGGgraph": { "name": "KEGGgraph", "version": "1.68.0", "sha256": "0cz2knpjhkq5b762gp4ahygd123ipdn1dlb4dkndd8n94gmfplyy", "depends": ["RCurl", "Rgraphviz", "XML", "graph"] }, "KEGGlincs": { "name": "KEGGlincs", "version": "1.34.0", "sha256": "1yl4vma9dsb2mw16r9n285chw3xgsjij1wmvd6msrspjc97cb37j", "depends": ["AnnotationDbi", "KEGGREST", "KEGGgraph", "KOdata", "RJSONIO", "XML", "gtools", "hgu133a_db", "httr", "igraph", "org_Hs_eg_db", "plyr"] }, "KinSwingR": { "name": "KinSwingR", "version": "1.26.0", "sha256": "0izs400ylnhzlqq0ln2v0977yixvncfv90lp9q4cxdh6332k6b54", "depends": ["BiocParallel", "data_table", "sqldf"] }, "KnowSeq": { "name": "KnowSeq", "version": "1.22.0", "sha256": "0k39fh0npnlj240y59wmzgg8fbfz7fkbafg5y2npjic68lqsp9pv", "depends": ["Hmisc", "R_utils", "XML", "caret", "cqn", "e1071", "edgeR", "ggplot2", "gridExtra", "httr", "jsonlite", "kernlab", "limma", "praznik", "randomForest", "reshape2", "rlist", "rmarkdown", "stringr", "sva"] }, "LACE": { "name": "LACE", "version": "2.12.0", "sha256": "1f1d9k4mxkv17p2p00rrxh4nr6sxbpkp6s5jmsh17cb52japn4sj", "depends": ["DT", "Matrix", "RColorBrewer", "Rfast", "SummarizedExperiment", "biomaRt", "bsplus", "callr", "configr", "curl", "data_table", "data_tree", "doParallel", "dplyr", "forcats", "foreach", "fs", "ggplot2", "htmltools", "htmlwidgets", "igraph", "jsonlite", "logr", "purrr", "readr", "shiny", "shinyBS", "shinyFiles", "shinydashboard", "shinyjs", "shinythemes", "shinyvalidate", "sortable", "stringi", "stringr", "svglite", "tidyr"] }, "LBE": { "name": "LBE", "version": "1.76.0", "sha256": "0r7xhzgmbm6jgsf95421gw8124g6j05kiv17c802a4k3dkdnp3ya", "depends": [] }, "LEA": { "name": "LEA", "version": "3.20.0", "sha256": "0n8mk1vgjlvrqasx1nsivypz76r4zl2k9d470s6973dyawzh2xxs", "depends": [] }, "LOBSTAHS": { "name": "LOBSTAHS", "version": "1.34.1", "sha256": "019m518sw3675fpj8szp5ww5jv1hl25kp7dxsk2zhfwz7pbj06cc", "depends": ["CAMERA", "xcms"] }, "LOLA": { "name": "LOLA", "version": "1.38.0", "sha256": "0k7fj7rv43df27n54v58d3j1jk1h1847klms1l63vhf32xlgdsnh", "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "data_table", "reshape2"] }, "LPE": { "name": "LPE", "version": "1.82.0", "sha256": "0r58af20b4mfwabm81rrkr55fzj7jwxhwmhj2lqz76h87jfwdfvh", "depends": [] }, "LRBaseDbi": { "name": "LRBaseDbi", "version": "2.18.1", "sha256": "1wpa7vw9in3whya5b6p6pd3ninrg405wymh8lfrz15djc73cfg7a", "depends": ["AnnotationDbi", "Biobase", "DBI", "RSQLite"] }, "LRcell": { "name": "LRcell", "version": "1.16.0", "sha256": "1jdkj1slrq37amnjaqb8c6swzcz0n857wwv82ac2lbi60a96dn7n", "depends": ["AnnotationHub", "BiocParallel", "ExperimentHub", "dplyr", "ggplot2", "ggrepel", "magrittr"] }, "LedPred": { "name": "LedPred", "version": "1.42.0", "sha256": "0v1f0y87wph6ycww1inz1wak2fvr28bas26sqvcc36wa0w5c6n7s", "depends": ["RCurl", "ROCR", "akima", "e1071", "ggplot2", "irr", "jsonlite", "plot3D", "plyr", "testthat"] }, "Lheuristic": { "name": "Lheuristic", "version": "1.0.0", "sha256": "1cxfzfdhhhzvaf2a0ky5vlibqvmv2wqwxlnj6pfgfb74hd26n005", "depends": ["Hmisc", "MultiAssayExperiment", "energy", "ggplot2", "ggpubr"] }, "LimROTS": { "name": "LimROTS", "version": "1.0.3", "sha256": "1c0yrivrz5l8if150dzvqx7cxfn582sdd0ls2a9r724xarp65hhw", "depends": ["BiocParallel", "S4Vectors", "SummarizedExperiment", "dplyr", "limma", "qvalue", "stringr"] }, "LinTInd": { "name": "LinTInd", "version": "1.12.0", "sha256": "0hk602dvj93j3nqplm8nrxy51xl59ynplif63w5scbvngnvhlc9y", "depends": ["BiocGenerics", "Biostrings", "IRanges", "S4Vectors", "ape", "cowplot", "data_tree", "dplyr", "ggnewscale", "ggplot2", "ggtree", "networkD3", "pheatmap", "purrr", "pwalign", "reshape2", "rlist", "stringdist", "stringr"] }, "LinkHD": { "name": "LinkHD", "version": "1.22.0", "sha256": "1389pp0i4ahbi4i370p0il9rwiqk9plxy2a7s1x0nsycnb0df63q", "depends": ["MultiAssayExperiment", "cluster", "data_table", "emmeans", "ggplot2", "ggpubr", "gridExtra", "reshape2", "rio", "scales", "vegan"] }, "Linnorm": { "name": "Linnorm", "version": "2.32.0", "sha256": "1qqiqk43ag6pgpf027p3w4cphcnx1l70h6pcvm1fh1pmjkr35859", "depends": ["MASS", "Rcpp", "RcppArmadillo", "Rtsne", "amap", "apcluster", "ellipse", "fastcluster", "fpc", "ggdendro", "ggplot2", "gmodels", "igraph", "limma", "mclust", "statmod", "vegan", "zoo"] }, "LiquidAssociation": { "name": "LiquidAssociation", "version": "1.62.0", "sha256": "077fp1knsanjc1ijraakp60q6icyzgqx6hhqnysgbgg2i53ra7d3", "depends": ["Biobase", "geepack", "org_Sc_sgd_db", "yeastCC"] }, "LoomExperiment": { "name": "LoomExperiment", "version": "1.26.1", "sha256": "08vqs1nj7il0gj4kxd64pln6hb4m26yaarckvkdxs8clgl90syg1", "depends": ["BiocIO", "DelayedArray", "GenomicRanges", "HDF5Array", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "rhdf5", "stringr"] }, "LymphoSeq": { "name": "LymphoSeq", "version": "1.36.0", "sha256": "0smb2fpixdxvf8rmvrzcpddqhf6q56qwxpkjq1432vlsxijmkhax", "depends": ["Biostrings", "LymphoSeqDB", "RColorBrewer", "UpSetR", "VennDiagram", "circlize", "data_table", "dplyr", "ggplot2", "ggtree", "ineq", "msa", "phangorn", "plyr", "reshape", "stringdist"] }, "M3C": { "name": "M3C", "version": "1.30.0", "sha256": "159123f7357hi59b1pmb3r1ckbd63gkj8ax93s73jvi2jkhx6921", "depends": ["Matrix", "Rtsne", "cluster", "corpcor", "doParallel", "doSNOW", "foreach", "ggplot2", "matrixcalc", "umap"] }, "M3Drop": { "name": "M3Drop", "version": "1.34.0", "sha256": "0aa3imi6j0nq1yk7b8iivyflxs83h3fqrys9cmhpi0nn6p5wyj1s", "depends": ["Hmisc", "Matrix", "RColorBrewer", "bbmle", "gplots", "irlba", "matrixStats", "numDeriv", "reldist", "scater", "statmod"] }, "MACSQuantifyR": { "name": "MACSQuantifyR", "version": "1.22.0", "sha256": "1xf8x90m4s334m6zgzyqqxbwpg46ly8d1m4d3pa49nnlq2a5i0b7", "depends": ["ggplot2", "ggrepel", "gridExtra", "lattice", "latticeExtra", "png", "prettydoc", "readxl", "rmarkdown", "rvest", "xml2"] }, "MACSr": { "name": "MACSr", "version": "1.16.0", "sha256": "1a9g40z16rwzq8aw0msgvjwqkxnjwpqm4m98n255vkw66fgdv08i", "depends": ["AnnotationHub", "ExperimentHub", "S4Vectors", "basilisk", "reticulate"] }, "MADSEQ": { "name": "MADSEQ", "version": "1.34.0", "sha256": "1fir4xvhg9n33wzq0s5191k9z1ywj02g8khz1337hp137i2vn6jy", "depends": ["BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VGAM", "VariantAnnotation", "coda", "preprocessCore", "rjags", "rtracklayer", "vcfR", "zlibbioc"] }, "MAGAR": { "name": "MAGAR", "version": "1.16.0", "sha256": "1m8q3xszwr2fw2wv1f4b0agxi8yk8n9dyq1fdil1480s22qc4yzn", "depends": ["HDF5Array", "RnBeads", "RnBeads_hg19", "RnBeads_hg38", "UpSetR", "argparse", "bigstatsr", "crlmm", "data_table", "doParallel", "ff", "igraph", "impute", "jsonlite", "plyr", "reshape2", "rjson", "snpStats"] }, "MAI": { "name": "MAI", "version": "1.14.0", "sha256": "1agndinb8dihfgp22x111vxg8y0lcm1ig7afi73czijjmdhwygj3", "depends": ["S4Vectors", "SummarizedExperiment", "caret", "doParallel", "e1071", "foreach", "future", "future_apply", "missForest", "pcaMethods", "tidyverse"] }, "MAIT": { "name": "MAIT", "version": "1.42.0", "sha256": "0rz7a8087pigsw4h1hm9cyd28ij6pqvyczgg7jiy4far0xsals52", "depends": ["CAMERA", "MASS", "Rcpp", "agricolae", "caret", "class", "e1071", "gplots", "pls", "plsgenomics", "xcms"] }, "MANOR": { "name": "MANOR", "version": "1.80.0", "sha256": "1kyg0ar2hvk5cqn8jxbzypw9rvzpkb2qkim6rdjb3dc01jaach1p", "depends": ["GLAD"] }, "MAPFX": { "name": "MAPFX", "version": "1.4.0", "sha256": "077qqgd196spi064wj0hgj7xlhkv6qwas87gxip84fa9vj7rs35a", "depends": ["Biobase", "ComplexHeatmap", "RColorBrewer", "Rfast", "circlize", "cowplot", "e1071", "flowCore", "ggplot2", "glmnetUtils", "gtools", "iCellR", "igraph", "pbapply", "reshape2", "stringr", "uwot", "xgboost"] }, "MAST": { "name": "MAST", "version": "1.33.0", "sha256": "00rpm0w3cndza5dbiss7bmx6vpy1fqxw1rci44yap2m7z482xbjg", "depends": ["Biobase", "BiocGenerics", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "abind", "data_table", "ggplot2", "plyr", "progress", "reshape2", "stringr"] }, "MBASED": { "name": "MBASED", "version": "1.42.0", "sha256": "0nq3p1wam0ms69w01j7j0myvamvbv5dsyz7gwxh3vs7j00wz6i5l", "depends": ["BiocGenerics", "BiocParallel", "GenomicRanges", "RUnit", "SummarizedExperiment"] }, "MBAmethyl": { "name": "MBAmethyl", "version": "1.42.0", "sha256": "1dq44ks1pzx9950w6fjn1wjhbir99s0llr1z47xwxr90p5zm9h6p", "depends": [] }, "MBCB": { "name": "MBCB", "version": "1.62.0", "sha256": "1z8y0hg4qybwazig81kmhvi2ii09afc4iaggjmmwaf3n1vfcpcr3", "depends": ["preprocessCore", "tcltk2"] }, "MBECS": { "name": "MBECS", "version": "1.12.0", "sha256": "01hjnbaxjzjrlygqajzjlahvdqbf42a8kisiqkk8a2vv93vg8xyj", "depends": ["Matrix", "cluster", "dplyr", "ggplot2", "gridExtra", "limma", "lme4", "lmerTest", "magrittr", "pheatmap", "phyloseq", "rmarkdown", "ruv", "sva", "tibble", "tidyr", "vegan"] }, "MBQN": { "name": "MBQN", "version": "2.20.0", "sha256": "1kfa4ahxszqazd9vqpwjsafn2x7bki2qh1mfsfi6b3ypqnzls9vs", "depends": ["BiocFileCache", "PairedData", "RCurl", "SummarizedExperiment", "ggplot2", "limma", "preprocessCore", "rappdirs", "rmarkdown", "xml2"] }, "MBttest": { "name": "MBttest", "version": "1.36.0", "sha256": "06b3fidffqk92p48wicddngf6n4d361fpg2rblyg8d4655scpym5", "depends": ["gplots", "gtools"] }, "MCbiclust": { "name": "MCbiclust", "version": "1.32.0", "sha256": "1dhdwx3zxvjc14vzgapwd8640l6i410i0mhxlba31lrgn5x2qla4", "depends": ["AnnotationDbi", "BiocParallel", "GGally", "GO_db", "WGCNA", "cluster", "ggplot2", "org_Hs_eg_db", "scales"] }, "MDTS": { "name": "MDTS", "version": "1.28.0", "sha256": "192l91jg1z52zsix988s2jx9ijlyd6i60mzwxr38gvr1i21rpyxc", "depends": ["Biostrings", "DNAcopy", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "stringr"] }, "MEAL": { "name": "MEAL", "version": "1.38.0", "sha256": "1agl6fa6ib8ynb7gi3bl12djj2zh3ppyvq8nwsrcki9nb5dz95kr", "depends": ["Biobase", "BiocGenerics", "GenomicRanges", "Gviz", "IRanges", "MultiDataSet", "S4Vectors", "SmartSVA", "SummarizedExperiment", "ggplot2", "isva", "limma", "matrixStats", "minfi", "missMethyl", "permute", "vegan"] }, "MEAT": { "name": "MEAT", "version": "1.20.0", "sha256": "1qn4pkljvddq171qpmd97c11xvvfk6nk3v5h0lg4vj8wh8f0ky0n", "depends": ["RPMM", "SummarizedExperiment", "dplyr", "dynamicTreeCut", "glmnet", "impute", "minfi", "stringr", "tibble", "wateRmelon"] }, "MEB": { "name": "MEB", "version": "1.22.0", "sha256": "12dgmfqcxx387kbhq03a89rqfz04yjypyr5qqw5yhh4kss4jvnhd", "depends": ["SingleCellExperiment", "SummarizedExperiment", "e1071", "edgeR", "scater", "wrswoR"] }, "MEDIPS": { "name": "MEDIPS", "version": "1.60.0", "sha256": "1rvwnsrdcj437zq7g6z05phw1yvwa0jycvqlgqw9q1yl59nyqfmz", "depends": ["BSgenome", "Biostrings", "DNAcopy", "GenomicRanges", "IRanges", "Rsamtools", "biomaRt", "edgeR", "gtools", "preprocessCore", "rtracklayer"] }, "MEDME": { "name": "MEDME", "version": "1.68.0", "sha256": "14z92ds6s99v5ahvxi764hg1zzwdai0823vpv230c6vzsc9751af", "depends": ["Biostrings", "MASS", "drc"] }, "MEIGOR": { "name": "MEIGOR", "version": "1.42.0", "sha256": "1f9nw1w31w31xlgw5xhk07c1kdh8ihl8ri8l1i6pzkq1n7iv9xn9", "depends": ["CNORode", "Rsolnp", "deSolve", "snowfall"] }, "MGFM": { "name": "MGFM", "version": "1.42.0", "sha256": "0y35ai43i85w4rfzlmdyfpskywi9w8nakxi04ra2g6mbnlnfxp8v", "depends": ["AnnotationDbi", "annotate"] }, "MGFR": { "name": "MGFR", "version": "1.34.0", "sha256": "02d2m9yj5yq66b638jrwavpy2fsl41chh3gb13b4k0sca120bbxb", "depends": ["annotate", "biomaRt"] }, "MGnifyR": { "name": "MGnifyR", "version": "1.4.0", "sha256": "17h6zckhd2l11yzqzk0nq9v066dfhbaicnngvygg8f7mvmlrbppn", "depends": ["BiocGenerics", "MultiAssayExperiment", "S4Vectors", "SummarizedExperiment", "TreeSummarizedExperiment", "ape", "dplyr", "httr", "mia", "plyr", "reshape2", "tidyjson", "urltools"] }, "MICSQTL": { "name": "MICSQTL", "version": "1.6.0", "sha256": "12ns11va32v6a41bqrksbs4mgppnv7zhlj6f911jxw952gghm406", "depends": ["BiocParallel", "S4Vectors", "SummarizedExperiment", "TCA", "TOAST", "dirmult", "ggplot2", "ggpubr", "ggridges", "glue", "magrittr", "nnls", "purrr"] }, "MIRA": { "name": "MIRA", "version": "1.30.0", "sha256": "1dpp2fwnp9yj69dq6c9d2fsxlvx2pq1k47lgbcvhckzn2h2m8cwx", "depends": ["Biobase", "BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "bsseq", "data_table", "ggplot2"] }, "MIRit": { "name": "MIRit", "version": "1.4.1", "sha256": "116l7y5lmv0d3aly24i8p3wwd4hhnwvar7cdq8g1j6ng5gc1jvm2", "depends": ["AnnotationDbi", "BiocFileCache", "BiocParallel", "DESeq2", "MultiAssayExperiment", "Rcpp", "Rgraphviz", "edgeR", "fgsea", "genekitr", "geneset", "ggplot2", "ggpubr", "graph", "graphite", "httr", "limma", "rlang"] }, "MLInterfaces": { "name": "MLInterfaces", "version": "1.88.1", "sha256": "0ygppd5g4ii9flq4lkx6wjcwp4a5ykz175v8kk9wb2gx3gr2mwwc", "depends": ["Biobase", "BiocGenerics", "MASS", "RColorBrewer", "Rcpp", "SummarizedExperiment", "annotate", "cluster", "fpc", "gbm", "gdata", "genefilter", "ggvis", "hwriter", "magrittr", "mlbench", "pls", "rpart", "sfsmisc", "shiny", "threejs"] }, "MLP": { "name": "MLP", "version": "1.56.0", "sha256": "18vcin3m27b0yschk4c6p3ljgcv26jfvfnxvi95pdqms200ykq3m", "depends": ["AnnotationDbi", "gplots"] }, "MLSeq": { "name": "MLSeq", "version": "2.26.0", "sha256": "1b1bv4p1z4kpldzla3yn0c52g66fnkr0nn1043niljc4b53lkv80", "depends": ["Biobase", "DESeq2", "SummarizedExperiment", "VennDiagram", "caret", "edgeR", "foreach", "ggplot2", "limma", "pamr", "plyr", "sSeq", "testthat", "xtable"] }, "MMDiff2": { "name": "MMDiff2", "version": "1.36.0", "sha256": "1fd8mzkmbxfs0px6vwi5zrzgaj23149mj4s2528p0dib6pakx1w3", "depends": ["BSgenome", "Biobase", "Biostrings", "GenomicRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "ggplot2", "locfit", "shiny"] }, "MMUPHin": { "name": "MMUPHin", "version": "1.22.0", "sha256": "0d8i9b6pjwz409jd46fm1n9h21hzg8zgzpvchywpyc1k896fvz4l", "depends": ["Maaslin2", "cowplot", "dplyr", "fpc", "ggplot2", "igraph", "metafor", "stringr", "tidyr"] }, "MODA": { "name": "MODA", "version": "1.34.0", "sha256": "1sgzwqh7445q1y6m1gslwhp14xqd2kqihdrmbjcw90ddbal0c249", "depends": ["AMOUNTAIN", "RColorBrewer", "WGCNA", "cluster", "dynamicTreeCut", "igraph"] }, "MOFA2": { "name": "MOFA2", "version": "1.18.0", "sha256": "111i10ppnv8nkh7q2jhiz7w3r6iyw23a3pmmx8cnb1lhbl1p38lk", "depends": ["DelayedArray", "HDF5Array", "RColorBrewer", "Rtsne", "basilisk", "corrplot", "cowplot", "dplyr", "forcats", "ggplot2", "ggrepel", "magrittr", "pheatmap", "reshape2", "reticulate", "rhdf5", "stringi", "tidyr", "uwot"] }, "MOGAMUN": { "name": "MOGAMUN", "version": "1.18.0", "sha256": "00cfx9m0b14bbci2j07vzmfcfwj5mbjsh9dxrvgwdmafiw0vvmfl", "depends": ["BiocParallel", "RCy3", "RUnit", "igraph", "stringr"] }, "MOMA": { "name": "MOMA", "version": "1.20.0", "sha256": "0fdhkb080hkwl7xzz3xmkfc21plhxji1mcnl8i6irdrl6azd1rcx", "depends": ["ComplexHeatmap", "MKmisc", "MultiAssayExperiment", "RColorBrewer", "circlize", "cluster", "dplyr", "ggplot2", "magrittr", "qvalue", "readr", "reshape2", "rlang", "stringr", "tibble", "tidyr"] }, "MOSClip": { "name": "MOSClip", "version": "1.2.2", "sha256": "1m69aywsksz05jbbvbvr2y5q12khydy9i0izcxl04gnf3790kgdf", "depends": ["AnnotationDbi", "ComplexHeatmap", "FactoMineR", "Matrix", "MultiAssayExperiment", "NbClust", "RColorBrewer", "S4Vectors", "SuperExactTest", "checkmate", "circlize", "corpcor", "coxrobust", "elasticnet", "gRbase", "ggplot2", "ggplotify", "graph", "graphite", "gridExtra", "igraph", "org_Hs_eg_db", "pheatmap", "qpgraph", "reshape", "survival", "survminer"] }, "MOSim": { "name": "MOSim", "version": "2.4.0", "sha256": "0fzk1zlhfxrmsw9lkl25zmaa9136kdj6mni4mgslik3ixkyg3w0x", "depends": ["HiddenMarkov", "IRanges", "Rcpp", "S4Vectors", "Seurat", "Signac", "cpp11", "dplyr", "edgeR", "ggplot2", "lazyeval", "matrixStats", "rlang", "scran", "stringi", "stringr", "zoo"] }, "MPAC": { "name": "MPAC", "version": "1.2.0", "sha256": "1yjrfwrickyj92qixbmg9aya22vlpcxb7fyklx491c85a5kyha5b", "depends": ["BiocParallel", "BiocSingular", "ComplexHeatmap", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "bluster", "circlize", "data_table", "fgsea", "fitdistrplus", "ggplot2", "ggraph", "igraph", "scales", "scran", "stringr", "survival", "survminer", "viridis"] }, "MPFE": { "name": "MPFE", "version": "1.44.0", "sha256": "0agif5jpqxids56m5a2866gw7ikk6w0x7yv05hy30ckjakx46fds", "depends": [] }, "MPRAnalyze": { "name": "MPRAnalyze", "version": "1.26.0", "sha256": "0zrjii1daf025544fpqvximl7imwpkijpnvm74yxdis2ip43y6c4", "depends": ["BiocParallel", "SummarizedExperiment", "progress"] }, "MSA2dist": { "name": "MSA2dist", "version": "1.12.0", "sha256": "0i5wq4882jjm16gyx0k0qzmrb7mlpk5nkfj6fnaazqbqs5nqssgw", "depends": ["Biostrings", "GenomicRanges", "IRanges", "Rcpp", "RcppThread", "ape", "doParallel", "dplyr", "foreach", "pwalign", "rlang", "seqinr", "stringi", "stringr", "tibble", "tidyr"] }, "MSPrep": { "name": "MSPrep", "version": "1.18.0", "sha256": "0nxynjxddz4wj4lvgn223gz25r38lbpk3sh53gpgp7ncmjsvmpjm", "depends": ["S4Vectors", "SummarizedExperiment", "VIM", "crmn", "dplyr", "magrittr", "missForest", "pcaMethods", "preprocessCore", "rlang", "stringr", "sva", "tibble", "tidyr"] }, "MSnID": { "name": "MSnID", "version": "1.42.0", "sha256": "11w8x37pzhk0849152mdkl00bfacxrgbgrgzcca0qybd10vpfx5p", "depends": ["AnnotationDbi", "AnnotationHub", "Biobase", "BiocGenerics", "BiocStyle", "Biostrings", "MSnbase", "ProtGenerics", "RUnit", "R_cache", "Rcpp", "data_table", "doParallel", "dplyr", "foreach", "ggplot2", "iterators", "msmsTests", "mzID", "mzR", "purrr", "reshape2", "rlang", "stringr", "tibble", "xtable"] }, "MSnbase": { "name": "MSnbase", "version": "2.34.1", "sha256": "00r4kpjf8y8l4jf4hjaxrcgzji2vbm0maqg2ybz5ifq9zk07mfhk", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "IRanges", "MALDIquant", "MASS", "MsCoreUtils", "PSMatch", "ProtGenerics", "Rcpp", "S4Vectors", "affy", "digest", "ggplot2", "impute", "lattice", "mzID", "mzR", "pcaMethods", "plyr", "scales", "vsn"] }, "MSstats": { "name": "MSstats", "version": "4.16.1", "sha256": "157njfvy42826w1i0148d9sz8ac24nxgpzgbvw012w4xi7v464vy", "depends": ["MASS", "MSstatsConvert", "Rcpp", "RcppArmadillo", "checkmate", "data_table", "ggplot2", "ggrepel", "gplots", "htmltools", "limma", "lme4", "marray", "plotly", "preprocessCore", "statmod", "survival"] }, "MSstatsBig": { "name": "MSstatsBig", "version": "1.6.0", "sha256": "0ry5pi8wy0ylncgcc9prmk57wka7z1vy7mzgqyflw4bqmcwa5mfz", "depends": ["DBI", "MSstats", "MSstatsConvert", "arrow", "dplyr", "readr", "sparklyr"] }, "MSstatsBioNet": { "name": "MSstatsBioNet", "version": "1.0.0", "sha256": "1gl7mx0x0jf90mmsggl8s6cp3r4g1agf6g2dzza9m0d8d05vzqzv", "depends": ["MSstats", "RCy3", "httr", "jsonlite", "r2r", "tidyr"] }, "MSstatsConvert": { "name": "MSstatsConvert", "version": "1.18.1", "sha256": "181s0cg3b65pkvgwb0w11fv7j9jaf6qp8fyy37vmbfkgfc1r5ihy", "depends": ["checkmate", "data_table", "log4r", "stringi"] }, "MSstatsLOBD": { "name": "MSstatsLOBD", "version": "1.16.0", "sha256": "0jyp7lrk2f99gmxv76s9pbp7npybm3ml7wd97mdms8vw82alk2p9", "depends": ["Rcpp", "ggplot2", "minpack_lm"] }, "MSstatsLiP": { "name": "MSstatsLiP", "version": "1.14.1", "sha256": "1dkiywwj8nj9hadjbhbgavkq4xczbvb9s3pwl01d4mig584j7cqc", "depends": ["Biostrings", "MSstats", "MSstatsConvert", "MSstatsPTM", "Rcpp", "checkmate", "data_table", "dplyr", "factoextra", "ggplot2", "ggpubr", "gridExtra", "purrr", "scales", "stringr", "tibble", "tidyr", "tidyverse"] }, "MSstatsPTM": { "name": "MSstatsPTM", "version": "2.10.1", "sha256": "0by9a7393c3rnam0i6qr5knw9spca0w42rx311pc9lbphh31i1i2", "depends": ["Biostrings", "MSstats", "MSstatsConvert", "MSstatsTMT", "Rcpp", "checkmate", "data_table", "dplyr", "ggplot2", "ggrepel", "gridExtra", "stringi", "stringr"] }, "MSstatsQC": { "name": "MSstatsQC", "version": "2.26.0", "sha256": "0xxzxpd889xfdjjyh3w19n4wpnhilp20b33jagyiphn7zjmhyiw3", "depends": ["MSnbase", "dplyr", "ggExtra", "ggplot2", "plotly", "qcmetrics"] }, "MSstatsQCgui": { "name": "MSstatsQCgui", "version": "1.28.0", "sha256": "0i1s7hl4xp4wzwgy05y4pa0arxpndagljchbd59jb15k30rlb170", "depends": ["MSstatsQC", "dplyr", "ggExtra", "gridExtra", "plotly", "shiny"] }, "MSstatsShiny": { "name": "MSstatsShiny", "version": "1.10.0", "sha256": "01ia4rzzgminlr3gxvcv7g4y5lqa481d93rmr4iack9b0mmmjbiq", "depends": ["DT", "Hmisc", "MSstats", "MSstatsConvert", "MSstatsPTM", "MSstatsTMT", "data_table", "dplyr", "ggplot2", "ggrepel", "gplots", "htmltools", "marray", "mockery", "plotly", "readxl", "shiny", "shinyBS", "shinybusy", "shinyjs", "tidyr", "uuid"] }, "MSstatsTMT": { "name": "MSstatsTMT", "version": "2.16.0", "sha256": "023xi2xq2ga9y7m6s4xgv9paj31j35g0yvz9wb9vnln410309bv8", "depends": ["MSstats", "MSstatsConvert", "checkmate", "data_table", "ggplot2", "htmltools", "limma", "lme4", "lmerTest", "plotly"] }, "MVCClass": { "name": "MVCClass", "version": "1.82.0", "sha256": "0k2xxflf9dvpzbr6kp4m5599biq4pjlypsaas93xb5275wmmjvfr", "depends": [] }, "MWASTools": { "name": "MWASTools", "version": "1.32.0", "sha256": "1n7iyay8l3gpqqa83h1fyl3lm51j6d8gkijrhpnj0amplg32j3n2", "depends": ["ComplexHeatmap", "KEGGREST", "KEGGgraph", "RCurl", "SummarizedExperiment", "boot", "car", "ggplot2", "glm2", "gridExtra", "igraph", "ppcor", "qvalue"] }, "Maaslin2": { "name": "Maaslin2", "version": "1.22.0", "sha256": "10hdjhi1ykk513hzvs0bi6avzghqmkqns8knhz3ycv7bj3ynp70x", "depends": ["MASS", "biglm", "car", "chemometrics", "cplm", "data_table", "dplyr", "edgeR", "ggplot2", "glmmTMB", "hash", "lme4", "lmerTest", "logging", "metagenomeSeq", "optparse", "pbapply", "pcaPP", "pheatmap", "pscl", "robustbase", "tibble", "vegan"] }, "Macarron": { "name": "Macarron", "version": "1.12.2", "sha256": "1gmpw9lf39hdvaqfwqkr3vbq32g5ik8i48njdfmq2f42kdmdpxy6", "depends": ["BiocParallel", "DelayedArray", "Maaslin2", "RJSONIO", "SummarizedExperiment", "WGCNA", "data_table", "dynamicTreeCut", "ff", "httr", "logging", "plyr", "psych", "xml2"] }, "MantelCorr": { "name": "MantelCorr", "version": "1.78.0", "sha256": "108sq7x47x4qwnzlypjak4wshja79hrd4njazp4fckfw8hd9ahsg", "depends": [] }, "MassArray": { "name": "MassArray", "version": "1.60.0", "sha256": "1hb3wpvbfiqxfvncxcqgxvb8g32zdsiryhp4zqmf47dq4k8xvz7z", "depends": [] }, "MassSpecWavelet": { "name": "MassSpecWavelet", "version": "1.74.0", "sha256": "1g5d13057g7mn2m33gpchm71jb38fs2kc667hj7ry4yc14750ji8", "depends": [] }, "MatrixGenerics": { "name": "MatrixGenerics", "version": "1.20.0", "sha256": "1ys0239gzg3lq12g954b9zwhyqasbny2w1ra452kaj4pqc5p1dpl", "depends": ["matrixStats"] }, "MatrixQCvis": { "name": "MatrixQCvis", "version": "1.16.0", "sha256": "1c230z0bkyk5ga2lc4imzjrgbqsria5xqyvv4i4sihggb8iwmfwg", "depends": ["ComplexHeatmap", "DT", "ExperimentHub", "Hmisc", "MASS", "Rtsne", "SummarizedExperiment", "UpSetR", "dplyr", "ggplot2", "htmlwidgets", "impute", "imputeLCMD", "limma", "pcaMethods", "plotly", "proDA", "rlang", "rmarkdown", "shiny", "shinydashboard", "shinyhelper", "shinyjs", "sva", "tibble", "tidyr", "umap", "vsn"] }, "MatrixRider": { "name": "MatrixRider", "version": "1.40.0", "sha256": "0lmrfwfcymf3anc9x3d6lb5rchkip5wn4sjxpiv88rzvw1qhfql3", "depends": ["Biostrings", "IRanges", "S4Vectors", "TFBSTools", "XVector"] }, "MeSHDbi": { "name": "MeSHDbi", "version": "1.44.0", "sha256": "11xcaj09yrc3ama11irpy65amgfj2x996ialjvxnf6vlz4dx5hb4", "depends": ["AnnotationDbi", "Biobase", "RSQLite"] }, "MeasurementError_cor": { "name": "MeasurementError.cor", "version": "1.80.0", "sha256": "10fj8lw7p86b4pm994i3g4b3djz74zwy4g42p74f6ld65ap141as", "depends": [] }, "Melissa": { "name": "Melissa", "version": "1.24.0", "sha256": "0y80p2jp4i7wsgqilaz1xkp573z97zxx0gwc7bg6d78bqsych11b", "depends": ["BPRMeth", "BiocStyle", "GenomicRanges", "MCMCpack", "ROCR", "assertthat", "cowplot", "data_table", "doParallel", "foreach", "ggplot2", "magrittr", "matrixcalc", "mclust", "mvtnorm", "truncnorm"] }, "Mergeomics": { "name": "Mergeomics", "version": "1.36.0", "sha256": "0v9dn19rx8q0vaysycv869al8krfv1s1xsi5rvkjw5f9nl7rlqph", "depends": [] }, "MesKit": { "name": "MesKit", "version": "1.18.0", "sha256": "1mq8gdnmw9hjz51pairm95hpxpbih6sk06xxk5z19bcwv10ykpf1", "depends": ["AnnotationDbi", "Biostrings", "ComplexHeatmap", "IRanges", "RColorBrewer", "S4Vectors", "ape", "circlize", "cowplot", "data_table", "dplyr", "ggplot2", "ggrepel", "ggridges", "mclust", "phangorn", "pracma", "tidyr"] }, "MetCirc": { "name": "MetCirc", "version": "1.38.0", "sha256": "05jd5vdfsjmh4zg77l6apjggda0yfrywzjg0i8584gbvwy93jrfx", "depends": ["MsCoreUtils", "S4Vectors", "Spectra", "amap", "circlize", "ggplot2", "scales", "shiny"] }, "MetID": { "name": "MetID", "version": "1.26.0", "sha256": "0sb67qwyyhzrqblrbgka07xh5wzf91cbnmhwjfca1959b09j44fw", "depends": ["ChemmineR", "Matrix", "devtools", "igraph", "stringr"] }, "MetMashR": { "name": "MetMashR", "version": "1.2.0", "sha256": "1505j1jvmgnrxpbpkyh6am0baqmy312sc0fkg1dgzimq6pmwm170", "depends": ["cowplot", "dplyr", "ggplot2", "ggthemes", "httr", "rlang", "scales", "struct"] }, "MetNet": { "name": "MetNet", "version": "1.26.1", "sha256": "1pqvlnxa721ncqqmxkc5yyz4rjgca32533fn77acqsa05xiljhwg", "depends": ["BiocParallel", "GENIE3", "GeneNet", "S4Vectors", "SummarizedExperiment", "bnlearn", "corpcor", "dplyr", "ggplot2", "parmigene", "psych", "rlang", "stabs", "tibble", "tidyr"] }, "MetaCyto": { "name": "MetaCyto", "version": "1.30.0", "sha256": "1whln405cwxzv0wa5vshjph64kga1l65sadqs2cxnvykdhfvrxyn", "depends": ["FlowSOM", "cluster", "fastcluster", "flowCore", "ggplot2", "metafor", "tidyr"] }, "MetaNeighbor": { "name": "MetaNeighbor", "version": "1.28.0", "sha256": "0fb3zljwcdpwssflpvw387zjfck0r5lg33lysvvbcz0993il6q5g", "depends": ["Matrix", "RColorBrewer", "SingleCellExperiment", "SummarizedExperiment", "beanplot", "dplyr", "ggplot2", "gplots", "igraph", "matrixStats", "tibble", "tidyr"] }, "MetaPhOR": { "name": "MetaPhOR", "version": "1.10.0", "sha256": "0vwvxmzqpf9y16slqcm5rjg5bk1x48h0zf6acaa5z97hijya0v09", "depends": ["RCy3", "RecordLinkage", "clusterProfiler", "ggplot2", "ggrepel", "pheatmap", "stringr"] }, "MetaboAnnotation": { "name": "MetaboAnnotation", "version": "1.12.0", "sha256": "0rdacrj5vdf0j2943biqkn0qbckrqa8ajl33b246pq55c8ndd76k", "depends": ["AnnotationHub", "BiocGenerics", "BiocParallel", "CompoundDb", "MetaboCoreUtils", "MsCoreUtils", "ProtGenerics", "QFeatures", "S4Vectors", "Spectra", "SummarizedExperiment"] }, "MetaboCoreUtils": { "name": "MetaboCoreUtils", "version": "1.16.1", "sha256": "0r8p8d3glxd2g12l8z8fis5vzxaj9m0b3ybvij4ciwky4amxjnmc", "depends": ["BiocParallel", "MsCoreUtils"] }, "MetaboDynamics": { "name": "MetaboDynamics", "version": "1.0.2", "sha256": "1kaasmn9qx8gd6kyw691a4v6ixznpds37j10694y3dq8rh7xa65y", "depends": ["BH", "KEGGREST", "Rcpp", "RcppEigen", "RcppParallel", "S4Vectors", "StanHeaders", "SummarizedExperiment", "dendextend", "dplyr", "dynamicTreeCut", "ggplot2", "rlang", "rstan", "rstantools", "stringr", "tidyr"] }, "MetaboSignal": { "name": "MetaboSignal", "version": "1.38.0", "sha256": "045l0n26qi9rng6rs1rvzd8nn34s5ssa9fhnzvkrdslkwvsdws8y", "depends": ["AnnotationDbi", "EnsDb_Hsapiens_v75", "KEGGREST", "KEGGgraph", "MWASTools", "RCurl", "biomaRt", "hpar", "igraph", "mygene", "org_Hs_eg_db"] }, "MethPed": { "name": "MethPed", "version": "1.36.0", "sha256": "0hvy4g3p1gx7jc5ff9xqy8ns3gv6b2jpiqw9c9skc8zv948z6z9f", "depends": ["Biobase", "randomForest"] }, "MethReg": { "name": "MethReg", "version": "1.18.0", "sha256": "0k3ji740r12kdjbrlrycjqw5z4ar106k6v18p68zqa1ppbcpmlsa", "depends": ["AnnotationHub", "DelayedArray", "ExperimentHub", "GenomicRanges", "IRanges", "JASPAR2024", "MASS", "Matrix", "RSQLite", "S4Vectors", "SummarizedExperiment", "TFBSTools", "dplyr", "ggplot2", "ggpubr", "openxlsx", "plyr", "progress", "pscl", "readr", "rlang", "sesame", "sesameData", "sfsmisc", "stringr", "tibble", "tidyr"] }, "MethTargetedNGS": { "name": "MethTargetedNGS", "version": "1.40.0", "sha256": "1n87jfs4pvhsr1qp1n1mnn9bibzm124ski7psq3gqrwkx7l9lwyz", "depends": ["Biostrings", "gplots", "pwalign", "seqinr", "stringr"] }, "MethylAid": { "name": "MethylAid", "version": "1.42.0", "sha256": "1y7i7xq2xblhbxsabwh8vhvmimf3s9jqs6q0vff94809rhmqaifj", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "RColorBrewer", "SummarizedExperiment", "ggplot2", "gridBase", "hexbin", "matrixStats", "minfi", "shiny"] }, "MethylMix": { "name": "MethylMix", "version": "2.38.0", "sha256": "10nlklml75clsndjm07sbab4pwkp4qxdd3bh05mmmhjg375c7gdy", "depends": ["RColorBrewer", "RCurl", "RPMM", "R_matlab", "data_table", "digest", "foreach", "ggplot2", "impute", "limma"] }, "MethylSeekR": { "name": "MethylSeekR", "version": "1.48.0", "sha256": "0yrzg7b6m5fhqd270wrjx0lhk7g5gr1spqhvpz15iddkzspi5sd5", "depends": ["BSgenome", "GenomicRanges", "IRanges", "geneplotter", "mhsmm", "rtracklayer"] }, "Mfuzz": { "name": "Mfuzz", "version": "2.68.0", "sha256": "0642fgqba2jr0ldfmngrn4nsdqd1qmsfalwbykgzpf5daq9bgrxv", "depends": ["Biobase", "e1071", "tkWidgets"] }, "MiChip": { "name": "MiChip", "version": "1.62.0", "sha256": "18wdspm6g8aj7gryha1sxda47yaq5prhr4099m0f9all6i3zkxx9", "depends": ["Biobase"] }, "MiPP": { "name": "MiPP", "version": "1.80.0", "sha256": "1z6giz0m2ri6iy9p5rcpjalnzl3j6aqiqhf5giy29shhyqnw4zmk", "depends": ["Biobase", "MASS", "e1071"] }, "MiRaGE": { "name": "MiRaGE", "version": "1.50.0", "sha256": "07qv210jk2wv83rc2fc3p9vk1lljyrl2hp6lpk7vx2g1x62qnvbx", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocManager", "S4Vectors"] }, "MicrobiomeProfiler": { "name": "MicrobiomeProfiler", "version": "1.14.0", "sha256": "183shj5jdxpmb4gihwilfi5k63bl162svazn5xlkhyz4lgp7lrfc", "depends": ["DT", "clusterProfiler", "config", "enrichplot", "ggplot2", "golem", "gson", "htmltools", "magrittr", "shiny", "shinyWidgets", "shinycustomloader", "yulab_utils"] }, "MicrobiotaProcess": { "name": "MicrobiotaProcess", "version": "1.20.1", "sha256": "0zdlk4dr4cx9086r8kvjaf2fji2smz5wziipn5bzzzbq0zs6gnk2", "depends": ["Biostrings", "MASS", "SummarizedExperiment", "ape", "cli", "coin", "data_table", "dplyr", "dtplyr", "foreach", "ggfun", "ggplot2", "ggrepel", "ggsignif", "ggstar", "ggtree", "ggtreeExtra", "magrittr", "patchwork", "pillar", "plyr", "rlang", "tibble", "tidyr", "tidyselect", "tidytree", "treeio", "vegan", "zoo"] }, "MineICA": { "name": "MineICA", "version": "1.48.0", "sha256": "1kcaj2gmm7m4cm5w6rik0dsqscf9sph3adxmk9hd00cmpav78vxb", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "GOstats", "Hmisc", "JADE", "RColorBrewer", "Rgraphviz", "annotate", "biomaRt", "cluster", "colorspace", "fastICA", "foreach", "fpc", "ggplot2", "graph", "gtools", "igraph", "lumi", "lumiHumanAll_db", "marray", "mclust", "plyr", "scales", "xtable"] }, "MinimumDistance": { "name": "MinimumDistance", "version": "1.52.1", "sha256": "0dy6853l4iwa8dals9wipcqczg8p3lgisssvqqz19wcbcx21bk46", "depends": ["Biobase", "BiocGenerics", "DNAcopy", "GenomeInfoDb", "GenomicRanges", "IRanges", "MatrixGenerics", "S4Vectors", "SummarizedExperiment", "VanillaICE", "data_table", "ff", "foreach", "lattice", "matrixStats", "oligoClasses"] }, "ModCon": { "name": "ModCon", "version": "1.16.0", "sha256": "0gz3gb0ljj2gvpgchr6v0lspx0ylfqbsw35s9pxry7qwwzybarx2", "depends": ["data_table"] }, "Modstrings": { "name": "Modstrings", "version": "1.24.0", "sha256": "15cqi11y7vwv3w8mzirrv4sn3mb6h18mfmjflbayvs0wk1ngnwwq", "depends": ["BiocGenerics", "Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "XVector", "crayon", "stringi", "stringr"] }, "MoleculeExperiment": { "name": "MoleculeExperiment", "version": "1.8.0", "sha256": "0x7960yn8qbrlf4rqjs8lqhnn8x5ricqm4lrypcn2a2yla9sbyf3", "depends": ["BiocParallel", "EBImage", "Matrix", "S4Vectors", "SpatialExperiment", "cli", "data_table", "dplyr", "ggplot2", "magrittr", "purrr", "rhdf5", "rjson", "rlang", "terra"] }, "Moonlight2R": { "name": "Moonlight2R", "version": "1.6.0", "sha256": "1rjldg6kh3iy5sbmj75j0n80hbl75capxv2yrqhabpm608gcax1d", "depends": ["AnnotationHub", "Biobase", "BiocGenerics", "ComplexHeatmap", "DOSE", "EpiMix", "ExperimentHub", "GEOquery", "GenomicRanges", "HiveR", "RColorBrewer", "RISmed", "circlize", "clusterProfiler", "data_table", "doParallel", "dplyr", "easyPubMed", "foreach", "fuzzyjoin", "ggplot2", "gplots", "magrittr", "org_Hs_eg_db", "parmigene", "purrr", "qpdf", "randomForest", "readr", "rlang", "rtracklayer", "seqminer", "stringr", "tibble", "tidyHeatmap", "tidyr", "withr"] }, "MoonlightR": { "name": "MoonlightR", "version": "1.34.0", "sha256": "0hkq4821cg5ks49qqi256dnmys2yl9c660qhbidhq2h7ja3m8smi", "depends": ["Biobase", "DOSE", "GEOquery", "HiveR", "RColorBrewer", "RISmed", "SummarizedExperiment", "TCGAbiolinks", "circlize", "clusterProfiler", "doParallel", "foreach", "gplots", "limma", "parmigene", "randomForest"] }, "Motif2Site": { "name": "Motif2Site", "version": "1.12.0", "sha256": "102qbjvv9bf0r6j26didxai0zv6aw5lzd8sh81khw9qbdbc9342w", "depends": ["BSgenome", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "MASS", "S4Vectors", "edgeR", "mixtools"] }, "MotifDb": { "name": "MotifDb", "version": "1.50.0", "sha256": "1i7ih5g6wc7d2phqgjcj97y21w59d78qz22ik0sxcv4nw1zhg826", "depends": ["BiocGenerics", "Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "rtracklayer", "splitstackshape"] }, "MotifPeeker": { "name": "MotifPeeker", "version": "1.0.0", "sha256": "1rhmb7b28y96zdh9cxnh2c8qr7y0v05lxj9lil7cphlv2vdx3vfp", "depends": ["BSgenome", "BiocFileCache", "BiocParallel", "Biostrings", "DT", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "SummarizedExperiment", "dplyr", "ggplot2", "heatmaply", "htmltools", "htmlwidgets", "memes", "plotly", "purrr", "rmarkdown", "rtracklayer", "tidyr", "universalmotif", "viridis"] }, "MouseFM": { "name": "MouseFM", "version": "1.18.0", "sha256": "0v3dr3jlihqpx50nfy0qm8gjkwg9lqikpwmkaj2qwa55k73iilml", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "biomaRt", "curl", "data_table", "dplyr", "ggplot2", "gtools", "httr", "jsonlite", "reshape2", "rlist", "scales", "tidyr"] }, "MsBackendMassbank": { "name": "MsBackendMassbank", "version": "1.16.1", "sha256": "03783makc8q3jpqmxx86ymhfb3q3679m8a1bvi8ad8z4n0yx4w3i", "depends": ["BiocParallel", "DBI", "IRanges", "MsCoreUtils", "ProtGenerics", "S4Vectors", "Spectra"] }, "MsBackendMetaboLights": { "name": "MsBackendMetaboLights", "version": "1.2.0", "sha256": "1drirfjdfc026a7v0ll09cbiwjyxb088vm08mclvg5jk4hm5agq7", "depends": ["BiocFileCache", "ProtGenerics", "S4Vectors", "Spectra", "curl", "progress"] }, "MsBackendMgf": { "name": "MsBackendMgf", "version": "1.16.0", "sha256": "0rwl5kmnvg31q7dgs2r5gkwwyn6n3yqcwxqcz4kc0yar85kgvmds", "depends": ["BiocParallel", "IRanges", "MsCoreUtils", "ProtGenerics", "S4Vectors", "Spectra"] }, "MsBackendMsp": { "name": "MsBackendMsp", "version": "1.12.0", "sha256": "0c9f0ghkmh1xhbs2bfyn7ydwgwbpjwdrawcyixydwl00k9nma2h5", "depends": ["BiocParallel", "IRanges", "MsCoreUtils", "ProtGenerics", "S4Vectors", "Spectra"] }, "MsBackendRawFileReader": { "name": "MsBackendRawFileReader", "version": "1.14.0", "sha256": "1783c06bx4fvz50c5x6c5wjd2427crlyq61jcgjz8x712d1ji7iq", "depends": ["BiocParallel", "IRanges", "MsCoreUtils", "ProtGenerics", "S4Vectors", "Spectra", "rawrr"] }, "MsBackendSql": { "name": "MsBackendSql", "version": "1.8.0", "sha256": "0ca8l2h7w7hhrnacd37b4bmqd3lmr01l08j3df78b0yf5fgbimb6", "depends": ["BiocGenerics", "BiocParallel", "DBI", "IRanges", "MsCoreUtils", "ProtGenerics", "S4Vectors", "Spectra", "data_table", "fastmatch", "progress", "stringi"] }, "MsCoreUtils": { "name": "MsCoreUtils", "version": "1.20.0", "sha256": "0xlnlgqmg8mzha8g6a6zhy735ia3dmnrrsyvlgv62n6bspcrh1g4", "depends": ["MASS", "Rcpp", "S4Vectors", "clue"] }, "MsDataHub": { "name": "MsDataHub", "version": "1.8.0", "sha256": "0b96yw687i3b0g00aaah2r2968iqashif4sd4a51nrzrf1vmpfsa", "depends": ["ExperimentHub"] }, "MsExperiment": { "name": "MsExperiment", "version": "1.10.1", "sha256": "18ig97c7clzsm0nj38gkl722130mkrb4k80hwjazyy8nx3civir0", "depends": ["BiocGenerics", "DBI", "IRanges", "ProtGenerics", "QFeatures", "S4Vectors", "Spectra", "SummarizedExperiment"] }, "MsFeatures": { "name": "MsFeatures", "version": "1.16.0", "sha256": "12hvv8pgahknhc4y1lkvrmgw1yr5v5j32nwad6pigi3c094pnir2", "depends": ["MsCoreUtils", "ProtGenerics", "SummarizedExperiment"] }, "MsQuality": { "name": "MsQuality", "version": "1.8.2", "sha256": "07yjack89qq6875b8f995r37wwnb0c3ldkfbx2wmi5f08i7rr687", "depends": ["BiocParallel", "MsExperiment", "ProtGenerics", "Spectra", "ggplot2", "htmlwidgets", "msdata", "plotly", "rlang", "rmzqc", "shiny", "shinydashboard", "stringr", "tibble", "tidyr"] }, "MuData": { "name": "MuData", "version": "1.12.0", "sha256": "1nf0mffw0r0z9l4pgssw1dc5v54nkmr6ccl9kg3fd7dpnkhlba70", "depends": ["DelayedArray", "Matrix", "MultiAssayExperiment", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "rhdf5"] }, "Mulcom": { "name": "Mulcom", "version": "1.58.0", "sha256": "1bbrcidbrp6i7a370gigdlmlf34qjlg6yxj4lcmfxy88qbk2rs3f", "depends": ["Biobase", "fields"] }, "MultiAssayExperiment": { "name": "MultiAssayExperiment", "version": "1.34.0", "sha256": "0nq9s319kdhi5rq886d1rpdww7bn06hm6d7298q8aqa6jaral2b3", "depends": ["Biobase", "BiocBaseUtils", "BiocGenerics", "DelayedArray", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "tidyr"] }, "MultiBaC": { "name": "MultiBaC", "version": "1.18.0", "sha256": "142h4wx5wyks9xfl30vxcj82sjzgrkkwjd6r16364z5b3cxlamsj", "depends": ["Matrix", "MultiAssayExperiment", "ggplot2", "pcaMethods", "plotrix", "ropls"] }, "MultiDataSet": { "name": "MultiDataSet", "version": "1.36.0", "sha256": "1a1d073nxwsfgw58aj0d5lsvky3p3jjxf1sa2csxqk2rkn0c0w5p", "depends": ["Biobase", "BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "ggplot2", "ggrepel", "limma", "qqman"] }, "MultiMed": { "name": "MultiMed", "version": "2.30.0", "sha256": "1rg3n2jli67dl5sgnbb987ax0vi31axx5n7hnmsvqngxd5iqpmff", "depends": [] }, "MultiRNAflow": { "name": "MultiRNAflow", "version": "1.6.0", "sha256": "04cwbf5ahyxn06055dn0jvif54y6d53yxxqjqrkr8f0r1ir2x2zg", "depends": ["Biobase", "ComplexHeatmap", "DESeq2", "FactoMineR", "Mfuzz", "S4Vectors", "SummarizedExperiment", "UpSetR", "factoextra", "ggalluvial", "ggplot2", "ggplotify", "ggrepel", "gprofiler2", "plot3D", "plot3Drgl", "reshape2"] }, "MultimodalExperiment": { "name": "MultimodalExperiment", "version": "1.8.0", "sha256": "0yl420p6wpq92vpn1ji84qimw20975cwc08354qp0ccw29c1msrq", "depends": ["BiocGenerics", "IRanges", "MultiAssayExperiment", "S4Vectors"] }, "MungeSumstats": { "name": "MungeSumstats", "version": "1.16.0", "sha256": "1raygfrqhpg4f1ifvc9f8ikb9p0mijc6l0mnlvz37bns9qgfip53", "depends": ["BSgenome", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "RCurl", "R_utils", "VariantAnnotation", "data_table", "dplyr", "ieugwasr", "rtracklayer", "stringr"] }, "MutationalPatterns": { "name": "MutationalPatterns", "version": "3.18.0", "sha256": "1mjjqhwzsma3yq21dvnrmmb5y5d25dng01wrmk850w30dg5lgq8j", "depends": ["BSgenome", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "NMF", "RColorBrewer", "S4Vectors", "VariantAnnotation", "cowplot", "dplyr", "ggalluvial", "ggdendro", "ggplot2", "magrittr", "pracma", "purrr", "stringr", "tibble", "tidyr"] }, "NADfinder": { "name": "NADfinder", "version": "1.32.0", "sha256": "0dv9x6dy0wiqqkydrvrp7lfxdlib7as62gl8ja6yhd29d1zg25ws", "depends": ["ATACseqQC", "BiocGenerics", "EmpiricalBrownsMethod", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "SummarizedExperiment", "baseline", "corrplot", "csaw", "limma", "metap", "rtracklayer", "signal", "trackViewer"] }, "NBAMSeq": { "name": "NBAMSeq", "version": "1.24.1", "sha256": "19lmjzxkdxb04rlkqilqimqhb1jrdgz2spjicsmcvl62rp5nnc15", "depends": ["BiocParallel", "DESeq2", "S4Vectors", "SummarizedExperiment", "genefilter", "mgcv"] }, "NCIgraph": { "name": "NCIgraph", "version": "1.56.0", "sha256": "1i4nqa84hi4f5c888rn8pzn1ysw1da1anl59rxvnfaaqs29svrsq", "depends": ["KEGGgraph", "RBGL", "RCy3", "R_oo", "graph"] }, "NOISeq": { "name": "NOISeq", "version": "2.52.0", "sha256": "1nd9dbjzvnpmpz107hjl3j4jq0yra13hk78lwz162xzr1275j0q4", "depends": ["Biobase", "Matrix"] }, "NPARC": { "name": "NPARC", "version": "1.20.0", "sha256": "0pggskl6nr0qjya95fk8ly0x9bhjx1a2avgchmwmv114lbi00di9", "depends": ["BiocParallel", "MASS", "broom", "dplyr", "magrittr", "rlang", "tidyr"] }, "NTW": { "name": "NTW", "version": "1.58.0", "sha256": "1an109y4gkrl3d65ssbd2s2cypc2cry75569marikms0pbb8iaid", "depends": ["mvtnorm"] }, "NanoMethViz": { "name": "NanoMethViz", "version": "3.4.0", "sha256": "0iiyihx60bjg4zl51ikljmw52p8g5y582zgzqj9xmwdlcvc1x7ws", "depends": ["AnnotationDbi", "BiocSingular", "Biostrings", "GenomicRanges", "IRanges", "R_utils", "Rcpp", "Rsamtools", "S4Vectors", "SummarizedExperiment", "assertthat", "bsseq", "cli", "cpp11", "dbscan", "dplyr", "e1071", "forcats", "fs", "ggplot2", "ggrastr", "glue", "limma", "patchwork", "purrr", "readr", "rlang", "scales", "stringr", "tibble", "tidyr", "withr"] }, "NanoStringDiff": { "name": "NanoStringDiff", "version": "1.38.0", "sha256": "0kfyrv0bkyhx8cp8q9jgsva7p44jng395r9g05gcn5cs9sz462g8", "depends": ["Biobase", "Rcpp", "matrixStats"] }, "NanoStringNCTools": { "name": "NanoStringNCTools", "version": "1.16.1", "sha256": "0bjjnxi7yp9r244mx7mcval71cn68ygbl48fzgqvic8dngymxfih", "depends": ["Biobase", "BiocGenerics", "Biostrings", "IRanges", "RColorBrewer", "S4Vectors", "ggbeeswarm", "ggiraph", "ggplot2", "ggthemes", "pheatmap"] }, "NanoTube": { "name": "NanoTube", "version": "1.14.0", "sha256": "06fcdly6r4kc51j3rbnx2zw2svp5j2ghwvlyabdsp9f7mbvicf21", "depends": ["Biobase", "fgsea", "ggplot2", "limma", "reshape"] }, "Nebulosa": { "name": "Nebulosa", "version": "1.18.0", "sha256": "0n2a8fhrqk9fsr3lc6mgl32iv3ydwj4ixv7p80v9xxi40fyxrzj2", "depends": ["Matrix", "SeuratObject", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "ggrastr", "ks", "patchwork"] }, "NetActivity": { "name": "NetActivity", "version": "1.10.0", "sha256": "1y3wrzijzm6anqjdwndbjcnjkyxkp5ayydw15grqz7yxld6w53bg", "depends": ["DESeq2", "DelayedArray", "DelayedMatrixStats", "NetActivityData", "SummarizedExperiment", "airway"] }, "NetPathMiner": { "name": "NetPathMiner", "version": "1.44.0", "sha256": "1k04y4bllfkx6w0i0sk6aiqmy9l6dmbpvwjlr8f8qxydb0w79082", "depends": ["igraph"] }, "NetSAM": { "name": "NetSAM", "version": "1.48.0", "sha256": "1km7jwqfmmkjjw35rpi8xx1p48ig06k0g2v53l27bygynfrfk7ig", "depends": ["AnnotationDbi", "DBI", "GO_db", "R2HTML", "WGCNA", "biomaRt", "doParallel", "foreach", "igraph", "seriation", "survival"] }, "NewWave": { "name": "NewWave", "version": "1.18.0", "sha256": "1ygy6biw62qbi6msgwbzmm18xz36ic38xxzhy4cl06b0j9dgzwwj", "depends": ["BiocSingular", "DelayedArray", "Matrix", "SharedObject", "SingleCellExperiment", "SummarizedExperiment", "irlba"] }, "NoRCE": { "name": "NoRCE", "version": "1.19.0", "sha256": "08kdwlxri7jsw0hvfbc2fv08qhwm6hkdyzplf5za4rhcrcyhzda4", "depends": ["AnnotationDbi", "DBI", "GO_db", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "KEGGREST", "RCurl", "RSQLite", "S4Vectors", "SummarizedExperiment", "biomaRt", "dbplyr", "dplyr", "ggplot2", "igraph", "png", "rWikiPathways", "reactome_db", "readr", "reshape2", "rtracklayer", "stringr", "tidyr", "zlibbioc"] }, "NormalyzerDE": { "name": "NormalyzerDE", "version": "1.26.0", "sha256": "1l1jm0rhcvgiscl061yr791p0dncskxm3yniajlrgjg9lpmdc7i1", "depends": ["MASS", "SummarizedExperiment", "ape", "car", "ggforce", "ggplot2", "limma", "matrixStats", "preprocessCore", "vsn"] }, "NormqPCR": { "name": "NormqPCR", "version": "1.54.0", "sha256": "0dg0idsx2v7nj7jg44adg2vw06405b1c4f288sdkpin6azak0i67", "depends": ["Biobase", "RColorBrewer", "ReadqPCR", "qpcR"] }, "NuPoP": { "name": "NuPoP", "version": "2.16.0", "sha256": "1giy3jjlcmhh99f1gmhsl2ifcvblzzglbd8kyp1k16i9n1dgb899", "depends": [] }, "OCplus": { "name": "OCplus", "version": "1.82.0", "sha256": "01s8jb6mh2ipxhnws05dv6r5b1m3cy196gf6szly1harg3wilm1q", "depends": ["interp", "multtest"] }, "OGRE": { "name": "OGRE", "version": "1.12.0", "sha256": "18hn4hjlfrxxzkw4mw6wymwwp3ivfp5zww6jypc9ncxx5pxjygj6", "depends": ["AnnotationHub", "DT", "GenomeInfoDb", "GenomicRanges", "Gviz", "IRanges", "S4Vectors", "assertthat", "data_table", "ggplot2", "rtracklayer", "shiny", "shinyBS", "shinyFiles", "shinydashboard", "tidyr"] }, "OLIN": { "name": "OLIN", "version": "1.86.0", "sha256": "09xrkawmsznjvpxb8xp59lb01q2lw7vsk9xyxdvrgila5fbvhb7k", "depends": ["limma", "locfit", "marray"] }, "OLINgui": { "name": "OLINgui", "version": "1.82.0", "sha256": "06j39p518jrp6xhcqwif3nkhf0xflxc6sk6x73642wx9q3cwml9d", "depends": ["OLIN", "marray", "tkWidgets", "widgetTools"] }, "OMICsPCA": { "name": "OMICsPCA", "version": "1.26.0", "sha256": "0iixl74v7q0xxl7k52dv5k7ly4nawmw24lcbcy9baf46xdq7cfiq", "depends": ["FactoMineR", "GenomeInfoDb", "HelloRanges", "IRanges", "MASS", "MultiAssayExperiment", "NbClust", "OMICsPCAdata", "PerformanceAnalytics", "clValid", "cluster", "corrplot", "cowplot", "data_table", "factoextra", "fpc", "ggplot2", "kableExtra", "magick", "pdftools", "reshape2", "rgl", "rmarkdown", "rtracklayer", "tidyr"] }, "OPWeight": { "name": "OPWeight", "version": "1.30.0", "sha256": "1jaflmghgh6pb26xnq4pp4cx0m63fa0nd0gaqaflswycxp1fkx0j", "depends": ["MASS", "qvalue", "tibble"] }, "ORFhunteR": { "name": "ORFhunteR", "version": "1.16.0", "sha256": "1rcs8rav0xhpx0fdx8i12q8zl4x2wa2d6kq0vvgx9md9nxpqcqjc", "depends": ["BSgenome_Hsapiens_UCSC_hg38", "Biostrings", "Peptides", "Rcpp", "data_table", "randomForest", "rtracklayer", "stringr", "xfun"] }, "ORFik": { "name": "ORFik", "version": "1.28.2", "sha256": "18s9jl7sxa5mwgz8j4s4g05fia77gr5ilrzvna5cr09pw4c892gv", "depends": ["AnnotationDbi", "BSgenome", "BiocFileCache", "BiocGenerics", "BiocParallel", "Biostrings", "DESeq2", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "R_utils", "Rcpp", "Rsamtools", "S4Vectors", "SummarizedExperiment", "XML", "biomaRt", "biomartr", "cowplot", "data_table", "fst", "ggplot2", "gridExtra", "httr", "jsonlite", "rtracklayer", "txdbmaker", "withr", "xml2"] }, "OSAT": { "name": "OSAT", "version": "1.56.0", "sha256": "119jncjfpmh2gswdd0cr9z2x2lr6sm0nsc0skpnmhkbhsrdw47la", "depends": [] }, "OSTA_data": { "name": "OSTA.data", "version": "1.0.0", "sha256": "07p6n49sykvs8hkhs0qkdhs8khgikqlyydjqm2mn7g06alakbmpn", "depends": ["BiocFileCache", "osfr"] }, "OTUbase": { "name": "OTUbase", "version": "1.58.0", "sha256": "1kq18jhivv2kpg91dz02pqfj1r3rxq61y7f2i2al965wqlhdjzni", "depends": ["Biobase", "Biostrings", "IRanges", "S4Vectors", "ShortRead", "vegan"] }, "OUTRIDER": { "name": "OUTRIDER", "version": "1.26.3", "sha256": "1kdr3ycxqxjl1ka9fij08cpj6ifmbrpmskgvr0c8wli52xkmi2vq", "depends": ["BBmisc", "BiocGenerics", "BiocParallel", "DESeq2", "GenomicFeatures", "GenomicRanges", "IRanges", "PRROC", "RColorBrewer", "RMTstat", "Rcpp", "RcppArmadillo", "S4Vectors", "SummarizedExperiment", "data_table", "generics", "ggplot2", "ggrepel", "heatmaply", "matrixStats", "pcaMethods", "pheatmap", "plotly", "plyr", "pracma", "reshape2", "scales", "txdbmaker"] }, "OVESEG": { "name": "OVESEG", "version": "1.24.0", "sha256": "1lc6k59f6v6rs3nd5him4lh2zq7rkzz12689dxpqys1kwn19ja99", "depends": ["BiocParallel", "Rcpp", "SummarizedExperiment", "fdrtool", "limma"] }, "OmaDB": { "name": "OmaDB", "version": "2.24.0", "sha256": "14b9xyhimvn4fmjvgd4qgzd6lq4k4bdw08w1wsivjkqd5s6fjs8k", "depends": ["Biostrings", "GenomicRanges", "IRanges", "ape", "httr", "jsonlite", "plyr", "topGO"] }, "OmicCircos": { "name": "OmicCircos", "version": "1.46.0", "sha256": "020m88v5msigzl448g5f89ijwjbdfbz9b33c4yhal05503zqjw2j", "depends": ["GenomicRanges"] }, "OmicsMLRepoR": { "name": "OmicsMLRepoR", "version": "1.2.0", "sha256": "0cfa80zylasvi7qbjiwsavl0yfn9ahji2sgzkfmi1lsbryppgyvc", "depends": ["BiocFileCache", "DiagrammeR", "data_tree", "dplyr", "jsonlite", "lubridate", "plyr", "readr", "rlang", "rols", "stringr", "tibble", "tidyr"] }, "Omixer": { "name": "Omixer", "version": "1.18.0", "sha256": "132mx5y60cqhpv584js7fk5qs9573jh0k6cmq4iikvqaxbf5x32v", "depends": ["dplyr", "forcats", "ggplot2", "gridExtra", "magrittr", "readr", "stringr", "tibble", "tidyselect"] }, "OmnipathR": { "name": "OmnipathR", "version": "3.16.0", "sha256": "0l5zbb05f4rgykmppwfsdah1f6601zqq67jsd5y1ck76sl2hq4gc", "depends": ["RSQLite", "R_utils", "XML", "checkmate", "crayon", "curl", "digest", "dplyr", "fs", "httr2", "igraph", "jsonlite", "later", "logger", "lubridate", "magrittr", "progress", "purrr", "rappdirs", "readr", "readxl", "rlang", "rmarkdown", "rvest", "sessioninfo", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "vctrs", "withr", "xml2", "yaml", "zip"] }, "OncoScore": { "name": "OncoScore", "version": "1.36.0", "sha256": "1nqyxl0l8q0v9nwp8nzjhmf5sdsiwmlrn3pwgg15da8s5i4j52kq", "depends": ["biomaRt"] }, "OncoSimulR": { "name": "OncoSimulR", "version": "4.10.0", "sha256": "1ps64p8svpfqxws7d3lzrkg3fymxnyhb5gsb88chncdixq2lfgp5", "depends": ["RColorBrewer", "Rcpp", "Rgraphviz", "car", "data_table", "dplyr", "ggplot2", "ggrepel", "graph", "gtools", "igraph", "smatr", "stringr"] }, "OpenStats": { "name": "OpenStats", "version": "1.20.0", "sha256": "0kbxpfjssb4ilkf8yw2xbzdhbp3sy8x68s2m5k3zpk8fiqhha04j", "depends": ["AICcmodavg", "Hmisc", "MASS", "car", "jsonlite", "knitr", "nlme", "rlist", "summarytools"] }, "OrderedList": { "name": "OrderedList", "version": "1.80.0", "sha256": "1hv3ffhwyc7y5d5ckdcn544v9k2bmd2axqs35ansqa2f1h9fhzv8", "depends": ["Biobase", "twilight"] }, "Organism_dplyr": { "name": "Organism.dplyr", "version": "1.36.0", "sha256": "03zb5w7pvgkgmszw3hryk18djpxdsvkns4klpj1d1fhxszh4m7x3", "depends": ["AnnotationDbi", "AnnotationFilter", "BiocFileCache", "DBI", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RSQLite", "S4Vectors", "dbplyr", "dplyr", "rlang", "tibble"] }, "OrganismDbi": { "name": "OrganismDbi", "version": "1.50.0", "sha256": "1lcxyb1xk81i4x4xjpbnkpbk2zfsbgw01q93i17fgahyrx2aa0d4", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocManager", "DBI", "GenomicFeatures", "GenomicRanges", "IRanges", "RBGL", "S4Vectors", "graph", "txdbmaker"] }, "Oscope": { "name": "Oscope", "version": "1.38.0", "sha256": "01m2rj837nmcvd1kiwxsdl76cdh0cjsdcyg8skkv1396s9716kj9", "depends": ["BiocParallel", "EBSeq", "cluster", "testthat"] }, "OutSplice": { "name": "OutSplice", "version": "1.8.0", "sha256": "01kgyvrw7xs9hinppxlf3xyj7whwl9hpp9xp7sjs1nhbcmjla2f2", "depends": ["AnnotationDbi", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "org_Hs_eg_db"] }, "PAA": { "name": "PAA", "version": "1.42.0", "sha256": "1grcf0859qnr7k4n8yj6f08jjfhc4fygj40sxnmqf0cyqqwn6djq", "depends": ["MASS", "ROCR", "Rcpp", "e1071", "gplots", "gtools", "limma", "mRMRe", "randomForest", "sva"] }, "PADOG": { "name": "PADOG", "version": "1.50.0", "sha256": "07bmnc1ajfr0dc4r6qnvkcxh39vhhwjx4bnai7mh0ni5z8aar1kz", "depends": ["AnnotationDbi", "Biobase", "GSA", "KEGGREST", "KEGGdzPathwaysGEO", "doRNG", "foreach", "hgu133a_db", "hgu133plus2_db", "limma", "nlme"] }, "PAIRADISE": { "name": "PAIRADISE", "version": "1.24.1", "sha256": "1b37cccspdjlgbbq22z7gr815b29m59kih1ikz7nb77xgln6gfjb", "depends": ["BiocParallel", "S4Vectors", "SummarizedExperiment", "abind", "nloptr"] }, "PANR": { "name": "PANR", "version": "1.54.0", "sha256": "1z4acn3y4rm1py0g8glvnwim1rpnagl31jx8x4h4c9wn3vi4lqi6", "depends": ["MASS", "RedeR", "igraph", "pvclust"] }, "PAST": { "name": "PAST", "version": "1.24.0", "sha256": "0qmws4g8km6zd0vn99q2v2c16g94p2zafsc05j6maram4kxwj5v7", "depends": ["GenomicRanges", "S4Vectors", "doParallel", "dplyr", "foreach", "ggplot2", "iterators", "qvalue", "rlang", "rtracklayer"] }, "PCAN": { "name": "PCAN", "version": "1.36.0", "sha256": "1q0jarcvqw9j83458ym9jl7qxh8175p39nhp9xbccy20p1gdx0yi", "depends": ["BiocParallel"] }, "PCAtools": { "name": "PCAtools", "version": "2.20.0", "sha256": "0jik25f4rpmr8gjy22i2myjhgsgqgslfjfskhv5bgkmqwbn931ar", "depends": ["BH", "BiocParallel", "BiocSingular", "DelayedArray", "DelayedMatrixStats", "Matrix", "Rcpp", "beachmat", "cowplot", "dqrng", "ggplot2", "ggrepel", "lattice", "reshape2"] }, "PDATK": { "name": "PDATK", "version": "1.16.1", "sha256": "0x3lc8ab1wgy6y78ab5myx3a7ip82zsfmyvls3n0zshnxi0acs6v", "depends": ["BiocGenerics", "BiocParallel", "ConsensusClusterPlus", "CoreGx", "MatrixGenerics", "MultiAssayExperiment", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "caret", "clusterRepro", "data_table", "dplyr", "genefu", "ggplot2", "ggplotify", "igraph", "matrixStats", "pROC", "piano", "plyr", "reportROC", "rlang", "scales", "survcomp", "survival", "survminer", "switchBox", "verification"] }, "PECA": { "name": "PECA", "version": "1.44.0", "sha256": "01w197gy41m03pj1xvhws8wl29r2jdrzmbrr4wqzfdia188xlbn1", "depends": ["ROTS", "affy", "aroma_affymetrix", "aroma_core", "genefilter", "limma", "preprocessCore"] }, "PICB": { "name": "PICB", "version": "1.0.0", "sha256": "1xafxl79c8srrp4kyjqmn475iw5p0clndssw27samkkjz4pr1k75", "depends": ["Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "data_table", "dplyr", "openxlsx", "seqinr"] }, "PICS": { "name": "PICS", "version": "2.51.0", "sha256": "1fchi92ka52902c4prscm85acw8f7sjihz2nx8lrc0qz421msdv7", "depends": ["GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools"] }, "PING": { "name": "PING", "version": "2.51.0", "sha256": "1fhw93llsslbn13679iph91klzpaqzi953zbxl4n9c9r2sbngsc9", "depends": ["BSgenome", "BiocGenerics", "GenomicRanges", "Gviz", "IRanges", "PICS", "S4Vectors", "fda"] }, "PIPETS": { "name": "PIPETS", "version": "1.4.0", "sha256": "08q4rrzs0zvjbdjx36xcp71xmxwwx5f03sq0zkz9rx1bdkc51v68", "depends": ["BiocGenerics", "GenomicRanges", "dplyr"] }, "PIUMA": { "name": "PIUMA", "version": "1.4.0", "sha256": "1g6ad3v8rw7rznbmqs0i31cjsl16m7cwhj43yhvrgyq4agcbc067", "depends": ["Hmisc", "SummarizedExperiment", "cluster", "dbscan", "ggplot2", "igraph", "kernlab", "patchwork", "scales", "tsne", "umap", "vegan"] }, "PLPE": { "name": "PLPE", "version": "1.68.0", "sha256": "06alwh01c6bxq7611grzy2qwv9591hpp34d86pb804sfdz9gs03z", "depends": ["Biobase", "LPE", "MASS"] }, "PLSDAbatch": { "name": "PLSDAbatch", "version": "1.4.0", "sha256": "1ac2zpim5r8v2cvqcs26w5n4vy30wzax3ph1rcd4kbxhm2m2z4ms", "depends": ["Biobase", "BiocStyle", "Rdpack", "TreeSummarizedExperiment", "ggplot2", "ggpubr", "gridExtra", "lmerTest", "mixOmics", "performance", "pheatmap", "scales", "vegan"] }, "POMA": { "name": "POMA", "version": "1.18.0", "sha256": "1sh3la8da590sd3vx736bpjjsq27f8p32g0qxrd3b8536i1223pd", "depends": ["ComplexHeatmap", "DESeq2", "FSA", "MASS", "RankProd", "SummarizedExperiment", "broom", "caret", "dbscan", "dplyr", "fgsea", "ggcorrplot", "ggplot2", "ggrepel", "glmnet", "impute", "janitor", "limma", "lme4", "magrittr", "mixOmics", "msigdbr", "multcomp", "purrr", "randomForest", "rlang", "sva", "tibble", "tidyr", "uwot", "vegan"] }, "POWSC": { "name": "POWSC", "version": "1.16.0", "sha256": "1y3kf1ngr4ri6p96xj4q0kqijsiwy53m5b6q0aqkgh60cb3h6lzq", "depends": ["Biobase", "MAST", "RColorBrewer", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "limma", "pheatmap"] }, "PPInfer": { "name": "PPInfer", "version": "1.34.0", "sha256": "0hw97rxbjxyhymgbwcikc0cq01jzl5019zrimwglrxlsm3b6r440", "depends": ["STRINGdb", "biomaRt", "fgsea", "ggplot2", "httr", "igraph", "kernlab", "yeastExpData"] }, "PREDA": { "name": "PREDA", "version": "1.54.0", "sha256": "1pfna5d18dd74zbl5xsd610mhanknkm7kfyq9sqfw4dyd0pajzbn", "depends": ["Biobase", "annotate", "lokern", "multtest"] }, "PROMISE": { "name": "PROMISE", "version": "1.60.0", "sha256": "1q8nm83fkrdl72hmzd8pfsi79ads20d05a4lhf1b7x6hd8107i4h", "depends": ["Biobase", "GSEABase"] }, "PRONE": { "name": "PRONE", "version": "1.2.1", "sha256": "00hmcdf5v3n4asynakd1zdpgda6bf8pia6kvccbb7y1dpbvhgks1", "depends": ["Biobase", "ComplexHeatmap", "ComplexUpset", "DEqMS", "MASS", "MSnbase", "NormalyzerDE", "POMA", "RColorBrewer", "ROTS", "S4Vectors", "SummarizedExperiment", "UpSetR", "circlize", "data_table", "dendsort", "dplyr", "edgeR", "ggplot2", "ggtext", "gprofiler2", "gtools", "limma", "magrittr", "matrixStats", "plotROC", "preprocessCore", "purrr", "reshape2", "scales", "stringr", "tibble", "tidyr", "vegan", "vsn"] }, "PROPER": { "name": "PROPER", "version": "1.40.0", "sha256": "0zsanqknfdx5x5p9x2f1n5l88201lxbwkniycfz11129dirma6j1", "depends": ["edgeR"] }, "PROPS": { "name": "PROPS", "version": "1.30.0", "sha256": "0nr49zqrnrwrpa488g9yiasy9azskkwpiyf7dh6r5wp1cdavab4y", "depends": ["Biobase", "bnlearn", "reshape2", "sva"] }, "PROcess": { "name": "PROcess", "version": "1.84.0", "sha256": "1bk87vp5kjw9kz8gibq8zisfx0qjiacgz5wvbq6mdddy1cl6a0xi", "depends": ["Icens"] }, "PSMatch": { "name": "PSMatch", "version": "1.12.0", "sha256": "1nz75m19g6jpvpm8ajx4hdyr03kg9h6yip5w4mjrnagyww4ksbkb", "depends": ["BiocGenerics", "BiocParallel", "IRanges", "Matrix", "MsCoreUtils", "ProtGenerics", "QFeatures", "S4Vectors", "Spectra", "igraph"] }, "PWMEnrich": { "name": "PWMEnrich", "version": "4.44.0", "sha256": "1zv08xi8r30j7pd4sqp3qciyjharqb4w3gryphf194l1jbd4lpds", "depends": ["BiocGenerics", "Biostrings", "S4Vectors", "evd", "gdata", "seqLogo"] }, "PanomiR": { "name": "PanomiR", "version": "1.12.0", "sha256": "1jjk39fa73jq1l330xbcrz15y0pqynx5nazhb755xhsd69g5r2v0", "depends": ["GSEABase", "RColorBrewer", "clusterProfiler", "dplyr", "forcats", "igraph", "limma", "metap", "org_Hs_eg_db", "preprocessCore", "rlang", "tibble", "withr"] }, "Path2PPI": { "name": "Path2PPI", "version": "1.38.0", "sha256": "1s8clrvnc56jzhc3q5dc7nxllzxf3dh8lykw2zxxqq082nhzgd5k", "depends": ["igraph"] }, "PathNet": { "name": "PathNet", "version": "1.48.0", "sha256": "11696s9q7kg72w0mgn82qm3hm4m86x37sgzp0s4sw0jmwi4nfh2q", "depends": [] }, "PathoStat": { "name": "PathoStat", "version": "1.34.0", "sha256": "1l2cxd8dhd6q6d35n4v3f6zl4gcigwak7bdc9lmdf3cximy12xp5", "depends": ["BiocStyle", "ComplexHeatmap", "DESeq2", "DT", "RColorBrewer", "ROCR", "XML", "ape", "corpcor", "devtools", "dplyr", "edgeR", "ggplot2", "glmnet", "gmodels", "knitr", "limma", "matrixStats", "phyloseq", "plotly", "plyr", "rentrez", "reshape2", "scales", "shiny", "shinyjs", "tidyr", "vegan", "webshot"] }, "PeacoQC": { "name": "PeacoQC", "version": "1.18.0", "sha256": "197yshr2c15rxp38q6dm5kwwgnwq1kkjlbavj1vqz7gghw020c6n", "depends": ["ComplexHeatmap", "circlize", "flowCore", "flowWorkspace", "ggplot2", "gridExtra", "plyr"] }, "Pedixplorer": { "name": "Pedixplorer", "version": "1.4.0", "sha256": "03i36mh6qwb0mppmx7vfaj5cr4l5xfdbbdskjxfmsb7dmxckx3bi", "depends": ["DT", "Matrix", "S4Vectors", "colourpicker", "data_table", "dplyr", "ggplot2", "gridExtra", "htmlwidgets", "plotly", "plyr", "quadprog", "readxl", "scales", "shiny", "shinyWidgets", "shinycssloaders", "shinytoastr", "stringr", "tidyr"] }, "PepSetTest": { "name": "PepSetTest", "version": "1.2.0", "sha256": "1c5fbwa9w83050ikjk8g8xy7zzjp9486n199i3xbrd2dn87da69f", "depends": ["MASS", "SummarizedExperiment", "dplyr", "limma", "lme4", "matrixStats", "reshape2", "tibble"] }, "PepsNMR": { "name": "PepsNMR", "version": "1.26.0", "sha256": "145a8979akhwd8j865j1x3fk81x64a5d5784hyi57cjsi5drgbk6", "depends": ["Matrix", "ggplot2", "gridExtra", "matrixStats", "ptw", "reshape2"] }, "PhIPData": { "name": "PhIPData", "version": "1.16.1", "sha256": "17sg9xbavd6vb7lr85chkg14j6x8zz6zifzss9w9pldmi8dyj2ds", "depends": ["BiocFileCache", "BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "cli", "edgeR"] }, "PharmacoGx": { "name": "PharmacoGx", "version": "3.12.2", "sha256": "1nx93z9xzyqfqxnilkc7351bk8n8kzvf5w4hhcnc1c2wcb32zraf", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "CoreGx", "MultiAssayExperiment", "RColorBrewer", "Rcpp", "S4Vectors", "SummarizedExperiment", "boot", "caTools", "checkmate", "coop", "data_table", "downloader", "ggplot2", "jsonlite", "magicaxis", "reshape2"] }, "PhenStat": { "name": "PhenStat", "version": "2.44.0", "sha256": "0gzhfy6mz3dazwy9hcb8ffgsfry6r4byl2a8b9qkir8ymv3q6s2p", "depends": ["MASS", "car", "corrplot", "ggplot2", "graph", "knitr", "lme4", "logistf", "msgps", "nlme", "nortest", "pingr", "reshape"] }, "PhenoGeneRanker": { "name": "PhenoGeneRanker", "version": "1.16.0", "sha256": "1a8x7yry49k891bfyv3ijillnzy1xfh2n11rz0mp07j6fy2sim26", "depends": ["Matrix", "doParallel", "dplyr", "foreach", "igraph"] }, "PhosR": { "name": "PhosR", "version": "1.18.1", "sha256": "157whkx3vnn6q8avn59ks8xhmr6fk8c0ffx12bspraxnf6d9al0g", "depends": ["BiocGenerics", "GGally", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "circlize", "dendextend", "dplyr", "e1071", "ggdendro", "ggplot2", "ggpubr", "ggtext", "igraph", "limma", "network", "pcaMethods", "pheatmap", "preprocessCore", "reshape2", "rlang", "ruv", "stringi", "tidyr"] }, "PhyloProfile": { "name": "PhyloProfile", "version": "2.0.6", "sha256": "0hdmz9zjl10wq6n29nvqyjfp0gr72iy115hcgfnavg1bkrfg5qv8", "depends": ["BiocStyle", "Biostrings", "DT", "RColorBrewer", "RCurl", "Rfast", "ape", "bioDist", "colourpicker", "data_table", "dplyr", "energy", "extrafont", "fastcluster", "ggplot2", "gridExtra", "htmlwidgets", "pbapply", "plotly", "scattermore", "shiny", "shinyBS", "shinyFiles", "shinycssloaders", "shinyjs", "stringr", "svglite", "tsne", "umap", "xml2", "yaml", "zoo"] }, "Pigengene": { "name": "Pigengene", "version": "1.34.0", "sha256": "02f1p69ci15r3l52g3fxvb4mfn4ldpl3vkh9710ynfdbn67dg0r9", "depends": ["BiocStyle", "C50", "DBI", "DOSE", "GO_db", "MASS", "ReactomePA", "Rgraphviz", "WGCNA", "bnlearn", "clusterProfiler", "dplyr", "gdata", "ggplot2", "graph", "impute", "matrixStats", "openxlsx", "partykit", "pheatmap", "preprocessCore"] }, "Pirat": { "name": "Pirat", "version": "1.2.0", "sha256": "0wky524d2j1qw80rwr8v211bqfkrdn4zfp5v2j8d24p9x3f9iyj6", "depends": ["MASS", "S4Vectors", "SummarizedExperiment", "basilisk", "ggplot2", "invgamma", "progress", "reticulate"] }, "PoDCall": { "name": "PoDCall", "version": "1.16.0", "sha256": "07cxwddq24gdm9ns78ahi5ak7kc4nz517gqkd011pf8pkrxnf8z3", "depends": ["DT", "LaplacesDemon", "diptest", "ggplot2", "gridExtra", "mclust", "purrr", "readr", "rlist", "shiny", "shinyjs"] }, "PolySTest": { "name": "PolySTest", "version": "1.2.0", "sha256": "0aplpw2vscnx92vi14dfvmw0cifhbpy3rsrvrhqj5zr6a1r4vpm4", "depends": ["S4Vectors", "SummarizedExperiment", "UpSetR", "circlize", "fdrtool", "gplots", "heatmaply", "knitr", "limma", "matrixStats", "plotly", "qvalue", "shiny"] }, "Polytect": { "name": "Polytect", "version": "1.0.0", "sha256": "0x28mwn6wxmxczl1zb10jxnnxrh5vdskjnyn30ymbwlgxblpagmb", "depends": ["BiocManager", "DiceKriging", "ParamHelpers", "cowplot", "dplyr", "flowPeaks", "ggplot2", "lhs", "mlrMBO", "mvtnorm", "rgenoud", "smoof", "sn", "tidyverse"] }, "PrInCE": { "name": "PrInCE", "version": "1.24.0", "sha256": "04vnigzbv4iz4739cgfwkvaxarqc3xvd4hbqz19ar85hmx65ljhj", "depends": ["Biobase", "Hmisc", "LiblineaR", "MSnbase", "Rdpack", "dplyr", "forecast", "magrittr", "naivebayes", "progress", "purrr", "ranger", "robustbase", "speedglm", "tester", "tidyr"] }, "Prostar": { "name": "Prostar", "version": "1.40.0", "sha256": "1jpdmr7xpxhfmig6hvld6b07idvd9zaxdnv5a9ghkd5afni37qr3", "depends": ["Biobase", "DAPAR", "DAPARdata", "DT", "RColorBrewer", "R_utils", "XML", "colourpicker", "data_table", "future", "ggplot2", "gplots", "gtools", "highcharter", "htmlwidgets", "later", "markdown", "promises", "rclipboard", "rhandsontable", "sass", "shiny", "shinyAce", "shinyBS", "shinyTree", "shinyWidgets", "shinycssloaders", "shinyjqui", "shinyjs", "shinythemes", "tibble", "vioplot", "webshot"] }, "ProtGenerics": { "name": "ProtGenerics", "version": "1.40.0", "sha256": "0a8niarfkb9jqamqj3ild5d2l6kc1amxgzn2aqk58w4whcip39i3", "depends": [] }, "ProteoDisco": { "name": "ProteoDisco", "version": "1.14.0", "sha256": "10rkzgas94rj2x8pdcyf488vlmfwlchblxrc1lxlq68f9xvs6i6l", "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "ParallelLogger", "S4Vectors", "VariantAnnotation", "XVector", "checkmate", "cleaver", "dplyr", "plyr", "rlang", "tibble", "tidyr"] }, "ProteoMM": { "name": "ProteoMM", "version": "1.26.0", "sha256": "1a40b6q8689s44kc2fd2gn0skcp4b4kfsn2ads3lsyx8nj0dgm69", "depends": ["biomaRt", "gdata", "ggplot2", "ggrepel", "gtools", "matrixStats"] }, "PureCN": { "name": "PureCN", "version": "2.14.1", "sha256": "1mjksg4dkrhdpz3254khy7miigi1z4clk383dz4wr1m5lpsqzw76", "depends": ["Biobase", "BiocGenerics", "Biostrings", "DNAcopy", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "RColorBrewer", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VGAM", "VariantAnnotation", "data_table", "futile_logger", "ggplot2", "gridExtra", "mclust", "rhdf5", "rtracklayer"] }, "Pviz": { "name": "Pviz", "version": "1.42.0", "sha256": "1n261ywz7hy8wrkflycarf122lnh4vllxvs1nvqwhdzxgsk96q6w", "depends": ["Biostrings", "GenomicRanges", "Gviz", "IRanges", "biovizBase", "data_table"] }, "QDNAseq": { "name": "QDNAseq", "version": "1.44.0", "sha256": "0zkdfs6axmw4qwr11q8mv8rdji1k64004r8w7ml789wn0chzdk4p", "depends": ["Biobase", "CGHbase", "CGHcall", "DNAcopy", "GenomicRanges", "IRanges", "R_utils", "Rsamtools", "future_apply", "matrixStats"] }, "QFeatures": { "name": "QFeatures", "version": "1.18.0", "sha256": "027qmi1cnbvjxzgyfhhm2kn3zgviw8w2px34jh85v7x4kbaxfwjb", "depends": ["AnnotationFilter", "Biobase", "BiocGenerics", "IRanges", "MsCoreUtils", "MultiAssayExperiment", "ProtGenerics", "S4Vectors", "SummarizedExperiment", "igraph", "lazyeval", "plotly", "reshape2", "tidyr", "tidyselect"] }, "QRscore": { "name": "QRscore", "version": "1.0.0", "sha256": "09bcsj415mcbzcliww5nc8vs2ki4a8pdalz0p8yjc3xkm8zwdskb", "depends": ["BiocParallel", "MASS", "arrangements", "assertthat", "dplyr", "hitandrun", "pscl"] }, "QSutils": { "name": "QSutils", "version": "1.26.0", "sha256": "0nx8hqpn1p0ny0hfzkajk4kws4vn22q9y2whn65cp7qy6z6fz42f", "depends": ["BiocGenerics", "Biostrings", "ape", "psych", "pwalign"] }, "QTLExperiment": { "name": "QTLExperiment", "version": "2.0.1", "sha256": "1q7r7qhx1sk1k0sq1dfgz791ab845k9acpgcqzw83y5q7d9cw809", "depends": ["BiocGenerics", "S4Vectors", "SummarizedExperiment", "ashr", "checkmate", "collapse", "dplyr", "rlang", "tibble", "tidyr", "vroom"] }, "QUBIC": { "name": "QUBIC", "version": "1.36.0", "sha256": "1xjr4idyfgddlrdcdhnkzbi1f9d42klqs661frckak21c6d7q009", "depends": ["Matrix", "Rcpp", "RcppArmadillo", "biclust"] }, "Qtlizer": { "name": "Qtlizer", "version": "1.22.0", "sha256": "12pdn4z3wiqivngrs5sw7y0zv8q25a9daw01vxm3z0vymfda8i6c", "depends": ["GenomicRanges", "curl", "httr", "stringi"] }, "QuasR": { "name": "QuasR", "version": "1.48.1", "sha256": "12rzljfqfz5sjwji4m6hbmgrlgj039rickvyvzryzxxh7kbzqk16", "depends": ["AnnotationDbi", "BSgenome", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicFiles", "GenomicRanges", "IRanges", "Rbowtie", "Rhtslib", "Rsamtools", "S4Vectors", "ShortRead", "rtracklayer", "txdbmaker"] }, "QuaternaryProd": { "name": "QuaternaryProd", "version": "1.42.0", "sha256": "03b7jw8w4ii3j1yga583bh1b26l9x7z7ah60lsp1mqaak9jida3q", "depends": ["Rcpp", "dplyr", "yaml"] }, "R3CPET": { "name": "R3CPET", "version": "1.40.0", "sha256": "1b21kbqrd53bhxxwxq4hbfd0v7gsmnjjnaain4s6lap1j5dlm99z", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "Hmisc", "IRanges", "RCurl", "Rcpp", "S4Vectors", "clValid", "data_table", "ggbio", "ggplot2", "igraph", "pheatmap", "reshape2"] }, "R453Plus1Toolbox": { "name": "R453Plus1Toolbox", "version": "1.58.0", "sha256": "1jc585yid6s9aw2if073hqi50wgmlr7g4pkdwvgrcsck45g7llfg", "depends": ["BSgenome", "Biobase", "BiocGenerics", "Biostrings", "GenomicRanges", "IRanges", "R2HTML", "Rsamtools", "S4Vectors", "ShortRead", "SummarizedExperiment", "TeachingDemos", "VariantAnnotation", "XVector", "biomaRt", "pwalign", "xtable"] }, "R4RNA": { "name": "R4RNA", "version": "1.36.0", "sha256": "1a34bxsn668ir8j8vkyp7s5chsji9yyv3wz3nrqnfq1pdmv6avlk", "depends": ["Biostrings"] }, "RAIDS": { "name": "RAIDS", "version": "1.6.1", "sha256": "10x9yfzj93agbc6hv2iymadl5jcxw7i8h571s3lw2wpq4wqzb0vp", "depends": ["AnnotationDbi", "AnnotationFilter", "BSgenome", "GENESIS", "GenomicRanges", "IRanges", "MatrixGenerics", "Rsamtools", "S4Vectors", "SNPRelate", "VariantAnnotation", "class", "dplyr", "ensembldb", "gdsfmt", "ggplot2", "pROC", "rlang", "stringr"] }, "RAREsim": { "name": "RAREsim", "version": "1.12.0", "sha256": "042k84jicjrp0ckzdxax036r0gi70y9ylkxfbyksmyzmlzrdsypf", "depends": ["nloptr"] }, "RBGL": { "name": "RBGL", "version": "1.84.0", "sha256": "0mp3xk2v7kf5c2pil6rjdz6s5adla9xrgk008hyj331gpgh6rq22", "depends": ["BH", "graph"] }, "RBM": { "name": "RBM", "version": "1.40.0", "sha256": "0yzjjf6qndrr66490mrfy9yk38d34lmdccfy14rckazwy595djlw", "depends": ["limma", "marray"] }, "RBioFormats": { "name": "RBioFormats", "version": "1.8.0", "sha256": "1nnlrzrw93vgn3xc1syg852mi0cbwydbrmagdksdca1c4bcmz3gh", "depends": ["EBImage", "S4Vectors", "rJava"] }, "RBioinf": { "name": "RBioinf", "version": "1.68.0", "sha256": "1q58rgg9mwnj47r945gpnpgdrp2hpkhfmgrs8w8hrqv718v2dx58", "depends": ["graph"] }, "RCAS": { "name": "RCAS", "version": "1.34.0", "sha256": "1p38q8qdbsy8aylv4m07srjs2zzblgmnyal55dd1bi7pxq2ifl2y", "depends": ["BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "BiocGenerics", "Biostrings", "DT", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RSQLite", "S4Vectors", "cowplot", "data_table", "genomation", "ggplot2", "gprofiler2", "knitr", "pbapply", "pheatmap", "plotly", "plotrix", "proxy", "ranger", "rmarkdown", "rtracklayer", "seqLogo", "txdbmaker"] }, "RCASPAR": { "name": "RCASPAR", "version": "1.54.0", "sha256": "15yzy4f16rvb1vpspzs85cr5lfx69340js0q32vj3gpfs5riakl9", "depends": [] }, "RCM": { "name": "RCM", "version": "1.24.0", "sha256": "0czpl1grlkjc66gnjnqkzz8r29p3i5m4m0mlpby3vlqp3gyb1k35", "depends": ["DBI", "MASS", "RColorBrewer", "VGAM", "alabama", "edgeR", "ggplot2", "nleqslv", "phyloseq", "reshape2", "tensor", "tseries"] }, "RCSL": { "name": "RCSL", "version": "1.16.0", "sha256": "0443frf0wvbjaw9b44j62ksbx8444a5607ldix7bqfdq49ys41ni", "depends": ["MatrixGenerics", "NbClust", "Rcpp", "RcppAnnoy", "Rtsne", "SingleCellExperiment", "ggplot2", "igraph", "pracma", "umap"] }, "RCX": { "name": "RCX", "version": "1.12.0", "sha256": "0vjjgz9l153g4k5phci7xi3w7xx3msjkhl3crb75qaldginlxj2n", "depends": ["igraph", "jsonlite", "plyr"] }, "RCy3": { "name": "RCy3", "version": "2.28.1", "sha256": "1r900ckrg82hdnk9f324dq1iihaf5y0nn1vhiybg7jmxbng9fcq5", "depends": ["BiocGenerics", "IRdisplay", "IRkernel", "RColorBrewer", "RCurl", "RJSONIO", "XML", "base64enc", "base64url", "fs", "glue", "gplots", "graph", "httr", "stringi", "uuid"] }, "RCyjs": { "name": "RCyjs", "version": "2.30.0", "sha256": "0kwfj1fy4plkgpghqbar7c99bandzgq88cjzrcr7y5k5ayq2i82r", "depends": ["BiocGenerics", "BrowserViz", "base64enc", "graph", "httpuv"] }, "RDRToolbox": { "name": "RDRToolbox", "version": "1.58.0", "sha256": "0z74xzh658ihg4rgyx83ywc18fa6gmiq2c5vilh4g0rgzhym8b22", "depends": ["MASS", "rgl"] }, "REBET": { "name": "REBET", "version": "1.26.0", "sha256": "06rrsv3ixafp44dyyc8p833488jnqs26xwp9x6ihr6j7bhkhlr7d", "depends": ["ASSET"] }, "REDseq": { "name": "REDseq", "version": "1.54.0", "sha256": "1n0z42gp1ar8qy3zrsw7fymykizaihr5azr9xafhn23vs14cbvxw", "depends": ["AnnotationDbi", "BSgenome", "BSgenome_Celegans_UCSC_ce2", "BiocGenerics", "Biostrings", "ChIPpeakAnno", "IRanges", "multtest"] }, "REMP": { "name": "REMP", "version": "1.32.1", "sha256": "18x0afk92q0imsc2fykqa2app0m9k81n318wf06rx5dsl74609aj", "depends": ["AnnotationHub", "BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "caret", "doParallel", "foreach", "impute", "iterators", "kernlab", "minfi", "org_Hs_eg_db", "ranger", "readr", "rtracklayer", "settings"] }, "RESOLVE": { "name": "RESOLVE", "version": "1.10.0", "sha256": "1xmngfmf6wivhrc7k382h270bnkmmd84ciz5824bfgn26apikgb2", "depends": ["BSgenome", "BSgenome_Hsapiens_1000genomes_hs37d5", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "MutationalPatterns", "RhpcBLASctl", "S4Vectors", "cluster", "data_table", "ggplot2", "glmnet", "gridExtra", "lsa", "nnls", "reshape2", "survival"] }, "RFLOMICS": { "name": "RFLOMICS", "version": "1.0.1", "sha256": "005lnnpjfqa0zbjw49wj48v9119wkq1dbcp6kdz7jwcb18cfizqc", "depends": ["AnnotationDbi", "ComplexHeatmap", "DT", "EnhancedVolcano", "FactoMineR", "MOFA2", "MultiAssayExperiment", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "UpSetR", "circlize", "clusterProfiler", "coseq", "data_table", "dplyr", "edgeR", "enrichplot", "ggplot2", "ggpubr", "ggrepel", "htmltools", "httr", "knitr", "limma", "magrittr", "mixOmics", "org_At_tair_db", "purrr", "reshape2", "reticulate", "rmarkdown", "shiny", "shinyBS", "shinyWidgets", "shinydashboard", "stringr", "tibble", "tidyr", "tidyselect", "vroom"] }, "RGSEA": { "name": "RGSEA", "version": "1.42.0", "sha256": "08xnvp9bgplilvkch5kwhgh42b4idbyk1ifjik8d66pmcpgh20ln", "depends": ["BiocGenerics"] }, "RGraph2js": { "name": "RGraph2js", "version": "1.36.0", "sha256": "0x12x6lhfmiypi3if91dzqgy7s80iwa0y74clj1g3vr9hyrfchix", "depends": ["digest", "graph", "rjson", "whisker"] }, "RITAN": { "name": "RITAN", "version": "1.32.0", "sha256": "0ah14512zk6dixis8h61p02hawjdkbxaizar9yzlw5i59b7q0mc2", "depends": ["AnnotationFilter", "BgeeDB", "EnsDb_Hsapiens_v86", "GenomicFeatures", "MCL", "RColorBrewer", "RITANdata", "STRINGdb", "dynamicTreeCut", "ensembldb", "ggplot2", "gplots", "gridExtra", "gsubfn", "hash", "igraph", "knitr", "plotrix", "png", "reshape2", "sqldf"] }, "RIVER": { "name": "RIVER", "version": "1.32.0", "sha256": "143xkc9pw91nnjc1ckj802mbq8fda6d1n36hb6f2zxjz8lvv4yb6", "depends": ["Biobase", "ggplot2", "glmnet", "pROC"] }, "RImmPort": { "name": "RImmPort", "version": "1.36.0", "sha256": "1rg3vlh06lzh3k95as0gn4hz11f0h62awd05fg1kzajxlq9g8pmk", "depends": ["DBI", "RSQLite", "data_table", "dplyr", "plyr", "reshape2", "sqldf"] }, "RJMCMCNucleosomes": { "name": "RJMCMCNucleosomes", "version": "1.32.0", "sha256": "0bl3kipfs0sn53215al0aq8388c285wx0skvlvcv43n9pi69q31y", "depends": ["BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rcpp", "S4Vectors", "consensusSeekeR"] }, "RLMM": { "name": "RLMM", "version": "1.70.0", "sha256": "08f3w217cqwa467kl5mp33f9vzy4ncx2wxjisl98ga6154ycyfjc", "depends": ["MASS"] }, "RLassoCox": { "name": "RLassoCox", "version": "1.16.0", "sha256": "0md18npzq5naddpzhdzx03kdz73173lv8bgrf1igbk59c0jh4psf", "depends": ["Matrix", "glmnet", "igraph", "survival"] }, "RMassBank": { "name": "RMassBank", "version": "3.18.0", "sha256": "1ndgm79033daiwlky5b0p3fd3sj2d0qv6nizs0z4wy2kszhwsasp", "depends": ["Biobase", "ChemmineR", "MSnbase", "R_utils", "Rcpp", "S4Vectors", "XML", "assertthat", "data_table", "digest", "dplyr", "enviPat", "glue", "httr", "httr2", "logger", "mzR", "purrr", "rcdk", "readJDX", "readr", "rjson", "tibble", "tidyselect", "webchem", "yaml"] }, "RNAAgeCalc": { "name": "RNAAgeCalc", "version": "1.20.0", "sha256": "0jqy569c2z09xsczsp2iq9dphcv99giy99yxpqw198ps9dx59a7p", "depends": ["AnnotationDbi", "SummarizedExperiment", "ggplot2", "impute", "org_Hs_eg_db", "recount"] }, "RNASeqPower": { "name": "RNASeqPower", "version": "1.48.0", "sha256": "1fgvgy3dqrpqp26f93d0bi97s5c4y43lhjlbqnjy97qh8iaaz2q8", "depends": [] }, "RNAdecay": { "name": "RNAdecay", "version": "1.28.0", "sha256": "10d1ciz37rxgkbi2hnqqq2cqkwrfflx1gcyjb5gl0zl8076rvy3m", "depends": ["TMB", "ggplot2", "gplots", "nloptr", "scales"] }, "RNAmodR": { "name": "RNAmodR", "version": "1.22.0", "sha256": "0xmbr3pfihxq6yhqcw0nrvl3zbxg6z6ajp7xyssa5gv5s52clr64", "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "Modstrings", "RColorBrewer", "ROCR", "Rsamtools", "S4Vectors", "colorRamps", "ggplot2", "matrixStats", "reshape2", "rtracklayer", "txdbmaker"] }, "RNAmodR_AlkAnilineSeq": { "name": "RNAmodR.AlkAnilineSeq", "version": "1.22.0", "sha256": "0kh4mdc6qhl3gdmpa34cxpcn9kplpvq8z47zcyhrm3ghw1gcajyr", "depends": ["BiocGenerics", "GenomicRanges", "Gviz", "IRanges", "RNAmodR", "S4Vectors"] }, "RNAmodR_ML": { "name": "RNAmodR.ML", "version": "1.22.0", "sha256": "1gc91kmnirkiisvizr8m9l16jlfb6zg5bkkjrlhz4i6yzscm8ljp", "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "RNAmodR", "S4Vectors", "ranger"] }, "RNAmodR_RiboMethSeq": { "name": "RNAmodR.RiboMethSeq", "version": "1.22.0", "sha256": "0sk74zkdfvf6pz2xxbga8fmp3r9sa4mk9zmd60j16049mhg6nicq", "depends": ["BiocGenerics", "GenomicRanges", "Gviz", "IRanges", "RNAmodR", "S4Vectors"] }, "RNAsense": { "name": "RNAsense", "version": "1.22.0", "sha256": "0x9njljjkmcb7nw27wf1ka31g7r4g8cd3pnlv33sc01fm1lzs53f", "depends": ["NBPSeq", "SummarizedExperiment", "ggplot2", "qvalue"] }, "RNAseqCovarImpute": { "name": "RNAseqCovarImpute", "version": "1.6.0", "sha256": "0phxjvg4ym8bcva22zyhq3rzi7jkv3m9af1spscpglcbs5kw4wcy", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "dplyr", "edgeR", "foreach", "limma", "magrittr", "mice", "rlang"] }, "ROC": { "name": "ROC", "version": "1.84.0", "sha256": "0bnw1n8bc03s0lfc6nlsbbzh2jkq95dvsfyv4dmxnr5cg5xvr6rm", "depends": ["knitr"] }, "ROCpAI": { "name": "ROCpAI", "version": "1.20.0", "sha256": "09lvnaf1ampnmknq5g5fb68rm9gy02bn3747zi3zrvlh2dx0v3dl", "depends": ["SummarizedExperiment", "boot", "fission", "knitr"] }, "ROSeq": { "name": "ROSeq", "version": "1.20.0", "sha256": "0dym341bbjwrc2w7ikiv92c6z27h107n32j1c7xjk0wjj6lji5nb", "depends": ["edgeR", "limma", "pbmcapply"] }, "ROTS": { "name": "ROTS", "version": "2.0.0", "sha256": "0y7n4bxw2945ygr1qk1yranvw57f2aspsk32hiyf3rhwvbl3vq2q", "depends": ["Biobase", "BiocParallel", "Rcpp", "lme4"] }, "ROntoTools": { "name": "ROntoTools", "version": "2.36.0", "sha256": "10gszx387x7clilzz31m0bmyh6r12q11585ayki0bmxfarkjp9jv", "depends": ["KEGGREST", "KEGGgraph", "Rgraphviz", "boot", "graph"] }, "RPA": { "name": "RPA", "version": "1.64.0", "sha256": "15v1dmz6vdmf7n90vx4v3lrxqb94mqs72i839dplalw75z3jb6ly", "depends": ["BiocGenerics", "BiocStyle", "affy", "phyloseq", "rmarkdown"] }, "RProtoBufLib": { "name": "RProtoBufLib", "version": "2.20.0", "sha256": "1vz9kdjdgcfipz743df4w060xzw2bx102ymps5j8x9brvjjp0h4q", "depends": [] }, "RRHO": { "name": "RRHO", "version": "1.48.0", "sha256": "16yxzb8919hj3bbbwmgrb56igcskdq6gcf4pdpvg2aflzpd44p9h", "depends": ["VennDiagram"] }, "RSVSim": { "name": "RSVSim", "version": "1.48.0", "sha256": "0ac7bs02jbdi0nmlrc60lb4j58291cvq8nnc5aa4y4gkmczzay28", "depends": ["Biostrings", "GenomicRanges", "IRanges", "ShortRead"] }, "RSeqAn": { "name": "RSeqAn", "version": "1.28.0", "sha256": "12a0vsykhsb948lgfvr378idhxg07kaxr7ipllya4nwcbghpfk1p", "depends": ["Rcpp"] }, "RTCA": { "name": "RTCA", "version": "1.60.0", "sha256": "09dzdxpkn29kpqx0av9xns53l1xfv3cs9r8vx3kf0rznag8ibm6r", "depends": ["Biobase", "RColorBrewer", "gtools"] }, "RTCGA": { "name": "RTCGA", "version": "1.38.0", "sha256": "0s7wyp8i7nqwpcvrg5w92q8k24qfh7n8cn8rk5nyg0wpfy3594z7", "depends": ["RCurl", "XML", "assertthat", "data_table", "dplyr", "ggplot2", "ggthemes", "htmltools", "knitr", "purrr", "rmarkdown", "rvest", "scales", "stringi", "survival", "survminer", "viridis", "xml2"] }, "RTCGAToolbox": { "name": "RTCGAToolbox", "version": "2.38.0", "sha256": "1b6f1v56mg59i1kzp63i57cqqw2d3ni8g6wbry7igf0k4r4ys401", "depends": ["BiocGenerics", "DelayedArray", "GenomeInfoDb", "GenomicRanges", "RCurl", "RJSONIO", "RaggedExperiment", "S4Vectors", "SummarizedExperiment", "TCGAutils", "data_table", "httr", "rvest", "stringr"] }, "RTN": { "name": "RTN", "version": "2.32.0", "sha256": "02w4szrmpf83n6bac763d2jn8d8aashi15zp30652c17s0l7i6vr", "depends": ["IRanges", "RedeR", "S4Vectors", "SummarizedExperiment", "car", "data_table", "igraph", "limma", "minet", "mixtools", "pheatmap", "pwr", "snow", "viper"] }, "RTNduals": { "name": "RTNduals", "version": "1.32.0", "sha256": "1zfig6q8rs93923fry7rjbipwcw6x5f7mfdmzvq3zp26x50yhkbj", "depends": ["RTN"] }, "RTNsurvival": { "name": "RTNsurvival", "version": "1.32.0", "sha256": "0l6kahakgygx1q8sn4naidnf2y5v7nx61d2bkikjlm8nbk3r0b34", "depends": ["RColorBrewer", "RTN", "RTNduals", "data_table", "dunn_test", "egg", "ggplot2", "pheatmap", "scales", "survival"] }, "RTopper": { "name": "RTopper", "version": "1.54.0", "sha256": "1prgabp4cxaswl6kqdpnp1928cmbw3vgw69wfjq342n08ldrmnm4", "depends": ["Biobase", "limma", "multtest"] }, "RUCova": { "name": "RUCova", "version": "1.0.0", "sha256": "15ampn6mdsi3gjrpa38f0j51fsmgfvl7nc00icfci8p95xbfn4f9", "depends": ["ComplexHeatmap", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "circlize", "dplyr", "fastDummies", "ggplot2", "magrittr", "stringr", "tibble", "tidyr", "tidyverse"] }, "RUVSeq": { "name": "RUVSeq", "version": "1.42.0", "sha256": "1b7f8zpkaz5h9ir8ajygnynh4n3ym4yd42vchjiv1w5zbc6q1s92", "depends": ["Biobase", "EDASeq", "MASS", "edgeR"] }, "RUVcorr": { "name": "RUVcorr", "version": "1.40.0", "sha256": "15jc2rbry8vgibsw5iivjnghzkdyjnqqvq9pfdklqp2ngwxqh26c", "depends": ["BiocParallel", "MASS", "bladderbatch", "corrplot", "gridExtra", "lattice", "psych", "reshape2", "snowfall"] }, "RUVnormalize": { "name": "RUVnormalize", "version": "1.42.0", "sha256": "13r06k8vwhj37bf7y9s2yanwa2z6avrsp9wy1q5gsrx8x5bds3va", "depends": ["Biobase", "RUVnormalizeData"] }, "RVS": { "name": "RVS", "version": "1.30.0", "sha256": "1v6rqj5prxiy9zh8xzgh0dwa2vb2sg2km36221jjijzf58h1gsb2", "depends": ["GENLIB", "R_utils", "gRain", "kinship2", "snpStats"] }, "RadioGx": { "name": "RadioGx", "version": "2.12.0", "sha256": "1jqyyzipabs4s245f4rsvv0pyxgjwan7hawkldqcldkvap9yw1za", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "CoreGx", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "assertthat", "caTools", "data_table", "downloader", "magicaxis", "matrixStats", "reshape2", "scales"] }, "RaggedExperiment": { "name": "RaggedExperiment", "version": "1.32.2", "sha256": "07jb7a95k2z2zpw0rrya1vr4rniwan9i1m9zf49z80rpqjykw0ix", "depends": ["BiocBaseUtils", "BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "Matrix", "MatrixGenerics", "S4Vectors", "SummarizedExperiment"] }, "RankProd": { "name": "RankProd", "version": "3.34.0", "sha256": "1dj2bgqkm82j0xx2wcdvh2gp42v15xjn8w5jymwslxhpqvzyvjdm", "depends": ["Rmpfr", "gmp"] }, "RareVariantVis": { "name": "RareVariantVis", "version": "2.36.0", "sha256": "1ycna49rl2ym79i8sdhndpz36glv96diwd5pblqcpk5zicnmq773", "depends": ["BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "BiocGenerics", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "GenomicScores", "IRanges", "S4Vectors", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg19_knownGene", "VariantAnnotation", "googleVis", "gtools", "phastCons100way_UCSC_hg19"] }, "Rarr": { "name": "Rarr", "version": "1.8.0", "sha256": "0xgy7crpl8cx4a31ka3nsvd58jhq3181ihrid69b9cxlbi5dx0r1", "depends": ["BiocGenerics", "DelayedArray", "R_utils", "httr", "jsonlite", "paws_storage", "stringr"] }, "RbcBook1": { "name": "RbcBook1", "version": "1.76.0", "sha256": "0skv22msidapcir87glhl29k1gw931yfar5927m4vk7rn2hv4qv3", "depends": ["Biobase", "graph", "rpart"] }, "Rbec": { "name": "Rbec", "version": "1.16.0", "sha256": "0whybz4pj99bpsfbxa1qa954cc888k5n7xmba5aj8f9zxk384hvd", "depends": ["Rcpp", "dada2", "doParallel", "foreach", "ggplot2", "readr"] }, "Rbowtie": { "name": "Rbowtie", "version": "1.48.0", "sha256": "0jcj8z1p2k993ngwyndv60gqm7kwsmc0wsazllgi1y68dxcawwav", "depends": [] }, "Rbowtie2": { "name": "Rbowtie2", "version": "2.14.0", "sha256": "0hg9xdybx3wnqgwf21df7mdabi73n5v8shw6jj4zx545g7j6sk95", "depends": ["Rsamtools", "magrittr"] }, "RbowtieCuda": { "name": "RbowtieCuda", "version": "1.0.1", "sha256": "0khl24jrx7r2qq1j08pfpmdij9csxvfh7qa7jgkmhm4miaxfyvvx", "depends": [] }, "Rbwa": { "name": "Rbwa", "version": "1.12.0", "sha256": "01qwndi4831l25l74rlq9jxzidslcf8yrwvqqsr633s33fr6cwa3", "depends": [] }, "RcisTarget": { "name": "RcisTarget", "version": "1.28.1", "sha256": "0w6ix0w8ns7yjzyri3dfl6m67hqvszlnczfj4i5w5yr0dp4k181b", "depends": ["AUCell", "BiocGenerics", "GSEABase", "GenomeInfoDb", "GenomicRanges", "R_utils", "S4Vectors", "SummarizedExperiment", "arrow", "data_table", "dplyr", "tibble", "zoo"] }, "Rcollectl": { "name": "Rcollectl", "version": "1.8.0", "sha256": "1c7xm74k1sdf4nc9js0pgigl984n38vik5xkhwb2fz14xz8ww4v6", "depends": ["ggplot2", "lubridate", "processx"] }, "Rcpi": { "name": "Rcpi", "version": "1.44.0", "sha256": "0apx48n35hsnavhpk19h0qif5918q81x862vs5m3b2l9dsizy10v", "depends": ["Biostrings", "GOSemSim", "curl", "doParallel", "foreach", "httr2", "jsonlite", "rlang"] }, "Rcwl": { "name": "Rcwl", "version": "1.24.0", "sha256": "1yk29i6kx722vgxnkgjj5jc0p3kiyd5gr3ixgcd8aph7ysfwnvbz", "depends": ["BiocParallel", "DiagrammeR", "R_utils", "S4Vectors", "basilisk", "batchtools", "codetools", "shiny", "yaml"] }, "RcwlPipelines": { "name": "RcwlPipelines", "version": "1.24.0", "sha256": "1jmyz3pxs9wb828laa38yz549hnl99c1nsgypdb1z4iqi5nn2n6i", "depends": ["BiocFileCache", "Rcwl", "S4Vectors", "git2r", "httr", "rappdirs"] }, "Rdisop": { "name": "Rdisop", "version": "1.68.0", "sha256": "0miqpygj9fk38qdxw51sr593hl131l9hx5kgjm71qq8wpwyd5ffd", "depends": ["Rcpp"] }, "ReUseData": { "name": "ReUseData", "version": "1.8.0", "sha256": "19sp94y9yik24wwvwjx2phvc79azlr0336g7b32xacb8q27vzvl5", "depends": ["BiocFileCache", "Rcwl", "RcwlPipelines", "S4Vectors", "basilisk", "jsonlite", "yaml"] }, "ReactomeGSA": { "name": "ReactomeGSA", "version": "1.22.0", "sha256": "1454alxr3hb9kmcbs6hsgqhds8cx11skw0fbxbdsf3jqn9niqvqy", "depends": ["Biobase", "BiocSingular", "RColorBrewer", "SummarizedExperiment", "dplyr", "ggplot2", "gplots", "httr", "igraph", "jsonlite", "progress", "tidyr"] }, "ReactomePA": { "name": "ReactomePA", "version": "1.52.0", "sha256": "0gh2p7c7kab84kyrqad9ai6ywnpc5l9zryizj939mc88akjywgdx", "depends": ["AnnotationDbi", "DOSE", "enrichplot", "ggplot2", "ggraph", "graphite", "gson", "igraph", "reactome_db", "yulab_utils"] }, "ReadqPCR": { "name": "ReadqPCR", "version": "1.54.0", "sha256": "0lzqr14rszkzhdg183kqpzamh2ii65rfrvb28iibzjmj0amp5khx", "depends": ["Biobase"] }, "RedeR": { "name": "RedeR", "version": "3.4.0", "sha256": "0nfnjhklhpsx149rqb0zldzs82nq39mhh4r3p1hl70ixk3xb3qbf", "depends": ["igraph", "scales"] }, "RedisParam": { "name": "RedisParam", "version": "1.10.0", "sha256": "1bangsygwq1g3ijh9g3cbjp9pa1axb19jcs927d3gw0mdrqq3cbv", "depends": ["BiocParallel", "futile_logger", "redux", "withr"] }, "ReducedExperiment": { "name": "ReducedExperiment", "version": "1.0.2", "sha256": "0mj7gv60scgb860parqzfp4z1yx7mdjfgym54li16rva89d4m793", "depends": ["BiocGenerics", "BiocParallel", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "WGCNA", "biomaRt", "car", "clusterProfiler", "ggplot2", "ica", "lme4", "lmerTest", "moments", "msigdbr", "patchwork", "pheatmap"] }, "RegEnrich": { "name": "RegEnrich", "version": "1.18.1", "sha256": "0gca99qzi1f4lhdijckn26rwd9vcigh0psqs9730d69x837m6vkr", "depends": ["BiocParallel", "BiocSet", "BiocStyle", "DESeq2", "DOSE", "S4Vectors", "SummarizedExperiment", "WGCNA", "dplyr", "fgsea", "ggplot2", "limma", "magrittr", "randomForest", "reshape2", "tibble"] }, "RegionalST": { "name": "RegionalST", "version": "1.6.0", "sha256": "003lpwgckxpnfqxi4ha5rm9djqy29r9yiwf23m5lcry8p6rwbjpx", "depends": ["BayesSpace", "BiocStyle", "RColorBrewer", "S4Vectors", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "TOAST", "assertthat", "colorspace", "dplyr", "fgsea", "ggplot2", "gridExtra", "magrittr", "scater", "shiny", "tibble"] }, "RepViz": { "name": "RepViz", "version": "1.24.0", "sha256": "0822djg1akxrbz02wvvyn54b25nsrnhvwprnj4nj5bz981gcbn2p", "depends": ["GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "biomaRt"] }, "Repitools": { "name": "Repitools", "version": "1.54.0", "sha256": "0k5vgpdnk4l0bi55dpidb2c6g13gyfia4xjzgsaliqaz3ss5w61x", "depends": ["BSgenome", "BiocGenerics", "Biostrings", "DNAcopy", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "MASS", "Rsamtools", "Rsolnp", "S4Vectors", "cluster", "edgeR", "gplots", "rtracklayer"] }, "ReportingTools": { "name": "ReportingTools", "version": "2.48.0", "sha256": "153y3v6wwdwn93m361xg6xb1nfl0v6px55p2rs2g08x82l5awmaj", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "Category", "DESeq2", "GOstats", "GSEABase", "IRanges", "PFAM_db", "R_utils", "XML", "annotate", "edgeR", "ggbio", "ggplot2", "hwriter", "knitr", "lattice", "limma"] }, "ResidualMatrix": { "name": "ResidualMatrix", "version": "1.18.0", "sha256": "0abf6i2z79d6jaa2ysibx9fx45f6chzra9q10s1rl02af6l6x3av", "depends": ["DelayedArray", "Matrix", "S4Vectors"] }, "Rfastp": { "name": "Rfastp", "version": "1.18.0", "sha256": "0lbfwgy5iv7jbbfgsijcyd7kfx7r5lpj3k5xypfdcx8cj9mm3ysb", "depends": ["Rcpp", "Rhtslib", "ggplot2", "reshape2", "rjson", "zlibbioc"] }, "RgnTX": { "name": "RgnTX", "version": "1.10.0", "sha256": "1vxpsnq94zddz3db62x69pmq7j9rwqgryh2zc116pgzk28hs98nm", "depends": ["GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "TxDb_Hsapiens_UCSC_hg19_knownGene", "ggplot2", "regioneR"] }, "Rgraphviz": { "name": "Rgraphviz", "version": "2.52.0", "sha256": "14capi4azvrk8lfidp8akp9l3nml5c4c0rv1j0wwbw3gqqvi1daz", "depends": ["graph"] }, "Rhdf5lib": { "name": "Rhdf5lib", "version": "1.30.0", "sha256": "0il7gj2msd25c4xmg5aw4z4y4gm1bzrdr9n0pn4h9k0nm7m0c1hp", "depends": [] }, "Rhisat2": { "name": "Rhisat2", "version": "1.24.0", "sha256": "04frc8xw60hvqkcss85pya2ajxrrwihlb5x0wwhhyf32rkfxl9q1", "depends": ["GenomicRanges", "SGSeq", "txdbmaker"] }, "Rhtslib": { "name": "Rhtslib", "version": "3.4.0", "sha256": "19y80cmm7njws4v30h55izm5qkvsz8hszm58i23xi8niw8s5qp47", "depends": [] }, "RiboCrypt": { "name": "RiboCrypt", "version": "1.13.0", "sha256": "0sxj27rpf43vqdf16k53msxxam16l1z441ndnqc1insx2ggkannp", "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "NGLVieweR", "ORFik", "RCurl", "bslib", "data_table", "dplyr", "ggplot2", "htmlwidgets", "httr", "jsonlite", "knitr", "markdown", "plotly", "rlang", "shiny", "shinycssloaders", "shinyhelper", "shinyjqui", "stringr"] }, "RiboDiPA": { "name": "RiboDiPA", "version": "1.16.0", "sha256": "1kmjkqvn2l8vrhd88y16kzkb7ff1l0kg6s3sp6r17mzgnv5873ij", "depends": ["BiocFileCache", "BiocGenerics", "DESeq2", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rcpp", "Rsamtools", "S4Vectors", "data_table", "doParallel", "elitism", "foreach", "ggplot2", "matrixStats", "qvalue", "reldist", "txdbmaker"] }, "RiboProfiling": { "name": "RiboProfiling", "version": "1.38.0", "sha256": "0yasqc6pqqxnhqfhwas1c9bm1820q716laq8fvdymah7l6x0gjb8", "depends": ["BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "data_table", "ggbio", "ggplot2", "plyr", "reshape2", "rtracklayer", "sqldf"] }, "Rigraphlib": { "name": "Rigraphlib", "version": "1.0.0", "sha256": "1fvr24vhnmbzvymqpbz2zsmxr2ii9j82j0v4s6g91lhz36z7fnx5", "depends": ["biocmake"] }, "Rmagpie": { "name": "Rmagpie", "version": "1.64.0", "sha256": "127jqfp2slhxj1h14w1gxs312nn4g30km6g6y5ishnh175lx2h2v", "depends": ["Biobase", "e1071", "kernlab", "pamr"] }, "Rmmquant": { "name": "Rmmquant", "version": "1.26.0", "sha256": "1ahpllp6illda2sh4nng3wgkdawmgx4wp7p4jgr7vr71m64vxwlw", "depends": ["BiocStyle", "DESeq2", "GenomicRanges", "Rcpp", "S4Vectors", "SummarizedExperiment", "TBX20BamSubset", "TxDb_Mmusculus_UCSC_mm9_knownGene", "apeglm", "devtools", "org_Mm_eg_db"] }, "RnBeads": { "name": "RnBeads", "version": "2.26.0", "sha256": "15vp5c40g1xlqvbwivc9zgiqm9ra5capbj37xpk0kjn8vl0qwa9x", "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "MASS", "S4Vectors", "cluster", "ff", "fields", "ggplot2", "gplots", "gridExtra", "illuminaio", "limma", "matrixStats", "methylumi", "plyr"] }, "RnaSeqSampleSize": { "name": "RnaSeqSampleSize", "version": "2.18.0", "sha256": "18w0jl42ra0xl90ym9ai0imr38gnw0vf1nksm9ymvj4mfaxmv51s", "depends": ["KEGGREST", "Rcpp", "RnaSeqSampleSizeData", "SummarizedExperiment", "biomaRt", "dplyr", "edgeR", "ggplot2", "ggpubr", "heatmap3", "matlab", "recount", "tidyr", "tidyselect"] }, "Rnits": { "name": "Rnits", "version": "1.42.0", "sha256": "1myjsg7gsp7ml64yahrbc3iyq2x07m8d9id24gg9p9z2lzafcnxk", "depends": ["Biobase", "affy", "boot", "ggplot2", "impute", "limma", "qvalue", "reshape2"] }, "RolDE": { "name": "RolDE", "version": "1.12.0", "sha256": "0l8mm8dmxy2jgpjfmkvfq60r34p3k489b4mp6zla2mmjvf0rllml", "depends": ["ROTS", "SummarizedExperiment", "doParallel", "doRNG", "foreach", "matrixStats", "nlme", "qvalue", "rngtools"] }, "Rqc": { "name": "Rqc", "version": "1.42.0", "sha256": "07n050h9gfzgs76dyk1q7gjlq5vqbp4j64fps7xp2xanwq8ppm0h", "depends": ["BiocGenerics", "BiocParallel", "BiocStyle", "Biostrings", "GenomicAlignments", "GenomicFiles", "IRanges", "Rcpp", "Rsamtools", "S4Vectors", "ShortRead", "biovizBase", "ggplot2", "knitr", "markdown", "plyr", "reshape2", "shiny"] }, "Rsamtools": { "name": "Rsamtools", "version": "2.24.0", "sha256": "183pish6qf0b8c76lx09hgmxy8j9sw3hh5nv5n6klx7r1y95k5id", "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rhtslib", "S4Vectors", "XVector", "bitops"] }, "Rsubread": { "name": "Rsubread", "version": "2.22.1", "sha256": "08721wn3savc7xwz4j7dv6vwc34xl1nsic3wvkb4h8pvwk1ix6q2", "depends": ["Matrix"] }, "Rtpca": { "name": "Rtpca", "version": "1.18.0", "sha256": "18ydwza5in3svszk4m73caki2asyqrzygr8vzg34x2nd5ylhincv", "depends": ["Biobase", "dplyr", "fdrtool", "ggplot2", "pROC", "tibble", "tidyr"] }, "Rtreemix": { "name": "Rtreemix", "version": "1.69.0", "sha256": "1sw0linj05wz2f9ax5809mcl1l7h16nvdk8xxl2pwgv78jkfzq8h", "depends": ["Biobase", "Hmisc", "graph"] }, "Rvisdiff": { "name": "Rvisdiff", "version": "1.6.0", "sha256": "15a7r82bv854alx1dciaa4lxr56pbqz1bs78qmrqy346q6n8369p", "depends": ["edgeR"] }, "S4Arrays": { "name": "S4Arrays", "version": "1.8.1", "sha256": "03y7yfym5xy0jg0c0ccmv3m1cbi4f96k3ny5p618xh309h1sizgi", "depends": ["BiocGenerics", "IRanges", "Matrix", "S4Vectors", "abind", "crayon"] }, "S4Vectors": { "name": "S4Vectors", "version": "0.46.0", "sha256": "0h3s32z6jxa118jifdyrhpj03fgjjh1fdnaq87ls38k7lg34jhn3", "depends": ["BiocGenerics"] }, "SAIGEgds": { "name": "SAIGEgds", "version": "2.8.0", "sha256": "1xrwi3i07gnaka4alm9v9n2ix38afdr98g4dhlv79lv0bwl44hq5", "depends": ["CompQuadForm", "Matrix", "Rcpp", "RcppArmadillo", "RcppParallel", "SeqArray", "gdsfmt", "survey"] }, "SANTA": { "name": "SANTA", "version": "2.44.0", "sha256": "1khvriq362n9my3w7k70rkwwpiv1b78mrclc6bgq8mzwlly136gm", "depends": ["Matrix", "igraph"] }, "SARC": { "name": "SARC", "version": "1.6.0", "sha256": "04g3pq9az8jfffgq19y8lzlhjrwi7gjlynfcpxpqsy8dk3gw5fwj", "depends": ["DescTools", "GenomicFeatures", "GenomicRanges", "IRanges", "RColorBrewer", "RaggedExperiment", "data_table", "ggplot2", "gridExtra", "gtable", "metap", "multtest", "plotly", "plyranges", "reshape2", "scales", "tidyverse"] }, "SBGNview": { "name": "SBGNview", "version": "1.22.0", "sha256": "06mq8m80670q3i046c1nmcabxnb9ahzygbshrpli19c4rq86wsy0", "depends": ["AnnotationDbi", "KEGGREST", "Rdpack", "SBGNview_data", "SummarizedExperiment", "bookdown", "httr", "igraph", "knitr", "pathview", "rmarkdown", "rsvg", "xml2"] }, "SBMLR": { "name": "SBMLR", "version": "2.4.0", "sha256": "0v4gcnqjb3vv7p0b9zmmqw58k567925xbjmk6sw9x1b31vn9wqnw", "depends": ["XML", "deSolve"] }, "SC3": { "name": "SC3", "version": "1.36.0", "sha256": "08akfziaczpzl7kvkchbr8a6w7qi7pnw0k4jklq0pyinx3ph713k", "depends": ["BiocGenerics", "ROCR", "Rcpp", "RcppArmadillo", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "WriteXLS", "cluster", "doParallel", "doRNG", "e1071", "foreach", "ggplot2", "pheatmap", "robustbase", "rrcov", "shiny"] }, "SCAN_UPC": { "name": "SCAN.UPC", "version": "2.50.0", "sha256": "1l5p9v780a3kh934xl3wi9wm7787ij70x8wsn9kag8p40813pzlw", "depends": ["Biobase", "Biostrings", "GEOquery", "IRanges", "MASS", "affy", "affyio", "foreach", "oligo", "sva"] }, "SCANVIS": { "name": "SCANVIS", "version": "1.22.0", "sha256": "162h8zcdw7ixqyql06sqgvcw0ydwlp1ahv3an1vzr0kw37vrshd0", "depends": ["IRanges", "RCurl", "plotrix", "rtracklayer"] }, "SCArray": { "name": "SCArray", "version": "1.16.0", "sha256": "0dcl2aaq5g822lkigqfcyfhpj7c56blbgnwdqlx6vj7g8wxhqrmb", "depends": ["BiocParallel", "BiocSingular", "DelayedArray", "DelayedMatrixStats", "Matrix", "S4Vectors", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "gdsfmt"] }, "SCArray_sat": { "name": "SCArray.sat", "version": "1.8.0", "sha256": "09i47n84pj5vmi8h9l4nd6nln4f9znl7iy0whvq477zfpijihf96", "depends": ["BiocGenerics", "BiocParallel", "BiocSingular", "DelayedArray", "Matrix", "S4Vectors", "SCArray", "Seurat", "SeuratObject", "SummarizedExperiment", "gdsfmt"] }, "SCBN": { "name": "SCBN", "version": "1.26.0", "sha256": "0d5kfkr2ljz27yfjxi98dc7ps2pdrkr9x5sw8dx0w38lsmm1zspc", "depends": [] }, "SCFA": { "name": "SCFA", "version": "1.18.0", "sha256": "1fbvjm9qm0bfz024262fb6ffsm2c39b8180isfxwfiwzafpqp67w", "depends": ["BiocParallel", "Matrix", "RhpcBLASctl", "cluster", "coro", "glmnet", "igraph", "matrixStats", "psych", "survival", "torch"] }, "SCOPE": { "name": "SCOPE", "version": "1.20.0", "sha256": "1fv8ryfqjwh94wfyya0w10bvgfqiwcvwand5r2kymkykgamrg6qn", "depends": ["BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "BiocGenerics", "Biostrings", "DNAcopy", "DescTools", "GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "doParallel", "foreach", "gplots"] }, "SCnorm": { "name": "SCnorm", "version": "1.30.1", "sha256": "0zc5cxax45gf4k0lwhzbfignqr6f410sya2mgz8ba5nn2fx4rmrl", "depends": ["BiocGenerics", "BiocParallel", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "cluster", "data_table", "forcats", "ggplot2", "moments", "quantreg"] }, "SDAMS": { "name": "SDAMS", "version": "1.28.0", "sha256": "1mdjwpik5hc03d18rp9gmmyxibqnkcb5vf4p4ljk80310sdmqh31", "depends": ["SummarizedExperiment", "qvalue", "trust"] }, "SELEX": { "name": "SELEX", "version": "1.40.0", "sha256": "1wjqpgrif5baqp3gfvvvb75g4jlqsaqsb5ql65gl43al79id7ih3", "depends": ["Biostrings", "rJava"] }, "SEraster": { "name": "SEraster", "version": "1.0.0", "sha256": "1wg14s4vam6c6plfzgn61x8f8xyvlfk4x6ryzw7vq6rpha1az2d8", "depends": ["BiocParallel", "Matrix", "SpatialExperiment", "SummarizedExperiment", "ggplot2", "rearrr", "sf"] }, "SEtools": { "name": "SEtools", "version": "1.22.0", "sha256": "05grm67znmjcmmj16pbk4r4zzlgly8h55504f6lnwlw656ic5vfi", "depends": ["BiocParallel", "DESeq2", "Matrix", "S4Vectors", "SummarizedExperiment", "circlize", "data_table", "edgeR", "openxlsx", "pheatmap", "sechm", "sva"] }, "SGCP": { "name": "SGCP", "version": "1.8.0", "sha256": "0jagx4ygl1sz32l4hskqn87qmnpqwdjj2y0basa07gapny3df879", "depends": ["DescTools", "GO_db", "GOstats", "RColorBrewer", "RSpectra", "Rgraphviz", "SummarizedExperiment", "annotate", "caret", "dplyr", "expm", "genefilter", "ggplot2", "ggridges", "graph", "openxlsx", "org_Hs_eg_db", "plyr", "reshape2", "xtable"] }, "SGSeq": { "name": "SGSeq", "version": "1.42.1", "sha256": "1lh6vwjpdm7gvyfyh3p2gqdwl7kg6vhl7l4cc0bfg2bmkvx8b2q9", "depends": ["AnnotationDbi", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "RUnit", "Rsamtools", "S4Vectors", "SummarizedExperiment", "igraph", "rtracklayer"] }, "SIAMCAT": { "name": "SIAMCAT", "version": "2.12.0", "sha256": "1z2lfa5dm8v8h9ld377bn4wd70663qwc9fcdgvr91danlfq9yldr", "depends": ["LiblineaR", "PRROC", "RColorBrewer", "beanplot", "corrplot", "glmnet", "gridBase", "gridExtra", "infotheo", "lgr", "lmerTest", "matrixStats", "mlr3", "mlr3learners", "mlr3tuning", "pROC", "paradox", "phyloseq", "progress", "scales", "stringr"] }, "SICtools": { "name": "SICtools", "version": "1.38.0", "sha256": "1f1dkrvnxqvcll1ywmckfi2glap0y2rilvw9y6s9qnlq21kcidy5", "depends": ["Biostrings", "GenomicRanges", "IRanges", "Rsamtools", "doParallel", "matrixStats", "plyr", "stringr"] }, "SIM": { "name": "SIM", "version": "1.78.0", "sha256": "0nlfg1m78idmfwzan435319i2x8my7lsdsjabaanpv54010kksam", "depends": ["globaltest", "quantreg", "quantsmooth"] }, "SIMAT": { "name": "SIMAT", "version": "1.40.0", "sha256": "1h7ny2c9sph0qd8dp0m7v273n3s87wzx18bhsbghns87s3h8d16q", "depends": ["Rcpp", "ggplot2", "mzR", "reshape2"] }, "SIMD": { "name": "SIMD", "version": "1.26.0", "sha256": "0ha591zbq14sibl67j3l3w32pachivh0g3fxq0fzdxzh9gdsmp69", "depends": ["edgeR", "methylMnM", "statmod"] }, "SIMLR": { "name": "SIMLR", "version": "1.34.0", "sha256": "19mziwmzhs40dnaqn6s6grlx3kjaggdnd97zy5brjhwlrx67vpfh", "depends": ["Matrix", "RSpectra", "Rcpp", "RcppAnnoy", "pracma"] }, "SLqPCR": { "name": "SLqPCR", "version": "1.74.0", "sha256": "0phhd8ih6s3fb5pkivjm9bmdn1mzjm30r44waza8a284kx2s7cir", "depends": [] }, "SMAD": { "name": "SMAD", "version": "1.24.0", "sha256": "0bs9sp6c4mn3r0gzxxbvj4qzqrc7igcl483m68jqvzximn52kv7y", "depends": ["Rcpp", "RcppAlgos", "dplyr", "magrittr", "tidyr"] }, "SMITE": { "name": "SMITE", "version": "1.36.0", "sha256": "11wv0xmhmxlff24ljqx4jsdbxa7h10kv2irzkyfi7mmpf8zxa2yf", "depends": ["AnnotationDbi", "BioNet", "Biobase", "GenomicRanges", "Hmisc", "IRanges", "KEGGREST", "S4Vectors", "geneLenDataBase", "ggplot2", "goseq", "igraph", "org_Hs_eg_db", "plyr", "reactome_db", "scales"] }, "SNAGEE": { "name": "SNAGEE", "version": "1.48.0", "sha256": "17n9vfgg1kk904244snlrmi7mcnd77h6afz10adf85ai015f4m9d", "depends": ["SNAGEEdata"] }, "SNPRelate": { "name": "SNPRelate", "version": "1.42.0", "sha256": "01lxwm9a1vzk1cmf3bcpgad60kgj49xwryzmjdgmvhjl3pckwdha", "depends": ["gdsfmt"] }, "SNPediaR": { "name": "SNPediaR", "version": "1.34.0", "sha256": "0v0n9y090x9r986dqqqx2h3p0byswhdnc6xq73yfimdihhcbj6k3", "depends": ["RCurl", "jsonlite"] }, "SNPhood": { "name": "SNPhood", "version": "1.38.0", "sha256": "0hp2gc6ab5sd0b29k37ncd4wsq8sncrcw37lvchyqjbi5bw38h7a", "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "DESeq2", "GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "checkmate", "cluster", "data_table", "ggplot2", "gridExtra", "lattice", "reshape2", "scales"] }, "SOMNiBUS": { "name": "SOMNiBUS", "version": "1.16.0", "sha256": "0lf9l4i4q5d19zyfk9cnfp0mqslf657vgqgy0ncgbdcwzjc0ln93", "depends": ["BiocManager", "GenomeInfoDb", "GenomicRanges", "IRanges", "Matrix", "S4Vectors", "VGAM", "annotatr", "bsseq", "data_table", "ggplot2", "mgcv", "reshape2", "rtracklayer", "tidyr", "yaml"] }, "SPEM": { "name": "SPEM", "version": "1.48.0", "sha256": "0zd61792n0zvjfhr2m75k0rqmpv0xfj3b231xpjs6fawm63ccr0p", "depends": ["Biobase", "Rsolnp"] }, "SPIA": { "name": "SPIA", "version": "2.60.0", "sha256": "1cyw7n54krb0867pn73jvdflslpx8848chpmiw7dvb82zpns43h0", "depends": ["KEGGgraph"] }, "SPIAT": { "name": "SPIAT", "version": "1.10.0", "sha256": "0jmjvvcqghbj8z5993803lb112safnkwv0cfygsxdpdanbddbc1x", "depends": ["RANN", "SpatialExperiment", "SummarizedExperiment", "apcluster", "dbscan", "dittoSeq", "dplyr", "ggplot2", "gridExtra", "gtools", "mmand", "pracma", "raster", "reshape2", "rlang", "sp", "spatstat_explore", "spatstat_geom", "tibble", "vroom"] }, "SPLINTER": { "name": "SPLINTER", "version": "1.34.0", "sha256": "09g7yyks7pd6lbaaivaizjs6xffavg8mw07pzkc2w1fb677ry10k", "depends": ["BSgenome_Mmusculus_UCSC_mm9", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "S4Vectors", "biomaRt", "ggplot2", "googleVis", "plyr", "pwalign", "seqLogo", "stringr"] }, "SPONGE": { "name": "SPONGE", "version": "1.30.0", "sha256": "1imz1avffk0dhvjgi6n6h445s9hpamdzr9kwc4bdy6ln4z1q8hwr", "depends": ["Biobase", "ComplexHeatmap", "MASS", "MetBrewer", "biomaRt", "caret", "cvms", "data_table", "doRNG", "dplyr", "expm", "foreach", "gRbase", "ggplot2", "ggpubr", "ggridges", "glmnet", "igraph", "iterators", "logging", "ppcor", "randomForest", "rlang", "stringr", "tidyr", "tidyverse", "tnet"] }, "SPOTlight": { "name": "SPOTlight", "version": "1.12.1", "sha256": "1kwx2nx6mh8sw6gj5m5w4i5cn056jxb4sf08jqnq9f0706arzrbp", "depends": ["Matrix", "Rcpp", "RcppEigen", "SingleCellExperiment", "ggplot2", "sparseMatrixStats"] }, "SPsimSeq": { "name": "SPsimSeq", "version": "1.18.0", "sha256": "0b0d6agni29c4w6r1bh149djy1cqqzwlvyvnz12q8sl02xjyiza6", "depends": ["Hmisc", "SingleCellExperiment", "WGCNA", "edgeR", "fitdistrplus", "limma", "mvtnorm", "phyloseq"] }, "SQLDataFrame": { "name": "SQLDataFrame", "version": "1.22.0", "sha256": "1hhllinhlb4byhjizkh68lk7rjxwgg1w7s4ngd99dlws814gav1z", "depends": ["BiocGenerics", "DBI", "DelayedArray", "RSQLite", "S4Vectors", "duckdb"] }, "SRAdb": { "name": "SRAdb", "version": "1.70.0", "sha256": "0hnq6pkzzs6s52lcqc3w4iqn19q72rwi25zn6mdvgihf6d7wdyxy", "depends": ["RCurl", "RSQLite", "R_utils", "graph"] }, "STATegRa": { "name": "STATegRa", "version": "1.44.0", "sha256": "07m4z817hf89qb7g95ry8vlwl49wfqw9whl7kp5v7j09g4bllxkx", "depends": ["Biobase", "MASS", "affy", "calibrate", "edgeR", "foreach", "ggplot2", "gplots", "gridExtra", "limma"] }, "STRINGdb": { "name": "STRINGdb", "version": "2.20.0", "sha256": "1dis3x4rx8g5wavgihbkhgvyb37cvjr6kdgyfi5lahnabxyyf6s8", "depends": ["RColorBrewer", "gplots", "hash", "httr", "igraph", "plotrix", "plyr", "png", "sqldf"] }, "SUITOR": { "name": "SUITOR", "version": "1.10.0", "sha256": "1gkg15r7xp47rmmzy8w38j04zfmfvi9ffr79zbzlkbchn9cp58a1", "depends": ["BiocParallel", "ggplot2"] }, "SVMDO": { "name": "SVMDO", "version": "1.8.0", "sha256": "15j8f66akb26rl5jygnb4kjr7py1a5f939ybwvllzmd5iz8lwsds", "depends": ["AnnotationDbi", "BSDA", "DOSE", "DT", "SummarizedExperiment", "caTools", "caret", "data_table", "dplyr", "e1071", "golem", "klaR", "nortest", "org_Hs_eg_db", "shiny", "shinyFiles", "shinytitle", "sjmisc", "survival"] }, "SVP": { "name": "SVP", "version": "1.0.2", "sha256": "14b21sixf25g5d41sb8rlx96w4qa7aydnnfkg95ah6bi88bn65aj", "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "DelayedMatrixStats", "Matrix", "Rcpp", "RcppArmadillo", "RcppEigen", "RcppParallel", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "cli", "deldir", "dplyr", "dqrng", "fastmatch", "ggfun", "ggplot2", "ggstar", "ggtree", "pracma", "rlang", "withr"] }, "SWATH2stats": { "name": "SWATH2stats", "version": "1.38.0", "sha256": "16jg3ny67wz3x0dx0gqf9npi60sl7r33g6rpsgs9j1bj32zgfkvd", "depends": ["biomaRt", "data_table", "ggplot2", "reshape2"] }, "SamSPECTRAL": { "name": "SamSPECTRAL", "version": "1.62.0", "sha256": "0si3m1dkv03d773irrcfvzk0zrkwzppwg4k5pk3iwhmmrimkpril", "depends": [] }, "Scale4C": { "name": "Scale4C", "version": "1.30.0", "sha256": "1fxmj3lsfgyvb5xka9wnmsdzdar04y9cgh987qmdsvpd96x8nvig", "depends": ["GenomicRanges", "IRanges", "SummarizedExperiment", "smoothie"] }, "ScaledMatrix": { "name": "ScaledMatrix", "version": "1.16.0", "sha256": "08q34yz58hcqjf4adnq0ihbrkiy04i3913bmmsr5giv0w6gywfx1", "depends": ["DelayedArray", "Matrix", "S4Vectors"] }, "Sconify": { "name": "Sconify", "version": "1.28.0", "sha256": "0mg5ffs28x78c4plp9307hsyrg5hhl9vgy9kn7zpa7dz3pv3x94y", "depends": ["FNN", "Rtsne", "dplyr", "flowCore", "ggplot2", "magrittr", "readr", "tibble"] }, "ScreenR": { "name": "ScreenR", "version": "1.10.0", "sha256": "10mbdr4bf4pv8m8d6smppr6yrcsdk1dkx87qb9rr6fqvf3xwvdsq", "depends": ["dplyr", "edgeR", "ggplot2", "ggvenn", "limma", "magrittr", "patchwork", "purrr", "rlang", "scales", "stringr", "tibble", "tidyr", "tidyselect"] }, "SemDist": { "name": "SemDist", "version": "1.42.0", "sha256": "15k53yb30h144rlrmw6c8v2y8cd67vn4jk393q1d9cj01g9h8q6b", "depends": ["AnnotationDbi", "GO_db", "annotate"] }, "SeqArray": { "name": "SeqArray", "version": "1.48.1", "sha256": "16vysi5lwlrl3k6hrk8a2hrgz799b5cis4w2h4mcgg8bg8wsgxxc", "depends": ["Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "digest", "gdsfmt"] }, "SeqGSEA": { "name": "SeqGSEA", "version": "1.48.0", "sha256": "1h8q0bhjcpsvwyd0s3z5jm8ggh5h9ay20aqayc1dpzs7fxj3n3fd", "depends": ["Biobase", "DESeq2", "biomaRt", "doParallel"] }, "SeqGate": { "name": "SeqGate", "version": "1.18.0", "sha256": "0i4l79ih9n9cz6cwsakzwalvc2ggdw5kcsfjr6v040y7086ki0mp", "depends": ["BiocManager", "GenomicRanges", "S4Vectors", "SummarizedExperiment"] }, "SeqSQC": { "name": "SeqSQC", "version": "1.30.0", "sha256": "0lilyycxf7idi0mjxwjiy454nnv01sm56jg319z1czn2873224pb", "depends": ["ExperimentHub", "GGally", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "SNPRelate", "e1071", "gdsfmt", "ggplot2", "plotly", "reshape2", "rmarkdown"] }, "SeqVarTools": { "name": "SeqVarTools", "version": "1.46.0", "sha256": "0d0fd7s7bwh19r4l70jbhskvjjgxl4k5kvwsx9hhv63f4ikrpvyh", "depends": ["Biobase", "BiocGenerics", "GWASExactHW", "GenomicRanges", "IRanges", "Matrix", "S4Vectors", "SeqArray", "data_table", "gdsfmt", "logistf"] }, "SharedObject": { "name": "SharedObject", "version": "1.22.0", "sha256": "17w14lpvd7ib917ym8gpwqvs7plmn6hrkyv41qcp1cqjphqz4s5c", "depends": ["BH", "BiocGenerics", "Rcpp"] }, "ShortRead": { "name": "ShortRead", "version": "1.66.0", "sha256": "1f3wnzdcd05aqxiz61lzhsbaigkpk3kgsvcjk97vgacagl925v3p", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rhtslib", "Rsamtools", "S4Vectors", "XVector", "hwriter", "lattice", "latticeExtra", "pwalign"] }, "SiPSiC": { "name": "SiPSiC", "version": "1.8.0", "sha256": "1annhw2y1zyvgg6rry25alqy0z3cpfk3nnd2xkr4fpgpl99jm44r", "depends": ["Matrix", "SingleCellExperiment"] }, "SigCheck": { "name": "SigCheck", "version": "2.40.0", "sha256": "1hgygkk7814wpqvq4qnfg0xas63ka7lwybrvdjx4046k2rxl0yl8", "depends": ["Biobase", "BiocParallel", "MLInterfaces", "e1071", "survival"] }, "SigFuge": { "name": "SigFuge", "version": "1.46.0", "sha256": "0x9px4mm24r2ffw1vd26rdm0ibv0023amsjhda59gkwxdgppkgj7", "depends": ["GenomicRanges", "ggplot2", "matlab", "reshape", "sigclust"] }, "SigsPack": { "name": "SigsPack", "version": "1.22.0", "sha256": "0bwx9mbmjvvspihhapcwiacn1m4gyvrg1xmr04ga4haywlp53pq3", "depends": ["BSgenome", "Biobase", "Biostrings", "GenomeInfoDb", "GenomicRanges", "SummarizedExperiment", "VariantAnnotation", "quadprog", "rtracklayer"] }, "SimBu": { "name": "SimBu", "version": "1.10.0", "sha256": "1cs8fkcpg7k0jpj2ajf8zpz92anrihsrkqig2w16fymn03v4hbrk", "depends": ["BiocParallel", "Matrix", "RColorBrewer", "RCurl", "SummarizedExperiment", "basilisk", "data_table", "dplyr", "ggplot2", "phyloseq", "proxyC", "reticulate", "sparseMatrixStats", "tidyr"] }, "SimFFPE": { "name": "SimFFPE", "version": "1.20.0", "sha256": "01v4aw3yf56sm5ashij69sw3hr4kbm6k9rmf2w76m47jck2hjhrr", "depends": ["Biostrings", "GenomicRanges", "IRanges", "Rsamtools", "doParallel", "dplyr", "foreach", "truncnorm"] }, "SingleCellAlleleExperiment": { "name": "SingleCellAlleleExperiment", "version": "1.4.1", "sha256": "1s04ndw94ax2y5ihw0kc9wj424jm5fdvyqg69hxnsy6af87k9r45", "depends": ["BiocParallel", "DelayedArray", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment"] }, "SingleCellExperiment": { "name": "SingleCellExperiment", "version": "1.30.1", "sha256": "0wfkyknyp4m0v49nn43l9invrr9ciwn6gz5vlh3gbkxha7d0643k", "depends": ["BiocGenerics", "DelayedArray", "GenomicRanges", "S4Vectors", "SummarizedExperiment"] }, "SingleCellSignalR": { "name": "SingleCellSignalR", "version": "1.20.0", "sha256": "0rv28vaiw02kbr8fpmd96w5170any1fmpz3pm6m3hbncgv27dz7q", "depends": ["BiocManager", "Rtsne", "circlize", "data_table", "edgeR", "foreach", "gplots", "igraph", "limma", "multtest", "pheatmap", "scran", "stringr"] }, "SingleMoleculeFootprinting": { "name": "SingleMoleculeFootprinting", "version": "2.2.0", "sha256": "05vqmxxl1c7bq5k8z3nih9z0yh9j56cscgv6ahkwz250faxgxc6x", "depends": ["BSgenome", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "Matrix", "QuasR", "RColorBrewer", "S4Vectors", "cluster", "dplyr", "ggplot2", "ggpointdensity", "ggrepel", "magrittr", "miscTools", "parallelDist", "patchwork", "plyranges", "rlang", "stringr", "tibble", "tidyr", "viridis"] }, "SingleR": { "name": "SingleR", "version": "2.10.0", "sha256": "0q5b8svzkif30ycpqdjibd04xzi3rj6nf8f9k2d339h711h0bmnf", "depends": ["BiocNeighbors", "BiocParallel", "DelayedArray", "DelayedMatrixStats", "Matrix", "Rcpp", "S4Vectors", "SummarizedExperiment", "assorthead", "beachmat"] }, "Site2Target": { "name": "Site2Target", "version": "1.0.0", "sha256": "1xw2kdl2sijrvs5dx5pq6ay52vz19sbc27g23ah01m41dg807p7z", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "MASS", "S4Vectors"] }, "SomaticSignatures": { "name": "SomaticSignatures", "version": "2.44.0", "sha256": "109y5kk68zshvvbac78anfzvx2wxcvi504n75paa277x9zmklixv", "depends": ["Biobase", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "NMF", "S4Vectors", "VariantAnnotation", "ggbio", "ggplot2", "pcaMethods", "proxy", "reshape2"] }, "SpaNorm": { "name": "SpaNorm", "version": "1.2.0", "sha256": "1ssvbmgid6lh29pfyymc97bpg5csf7rzhf39y8nxs40igknn9fz9", "depends": ["Matrix", "S4Vectors", "SeuratObject", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "edgeR", "ggplot2", "matrixStats", "rlang", "scran"] }, "SpaceMarkers": { "name": "SpaceMarkers", "version": "1.4.0", "sha256": "03xwlilzx9568mqdcap5ynhjvaslgxm3v1cwc28a3k2v6iqpmqdv", "depends": ["Matrix", "ape", "ggplot2", "hdf5r", "jsonlite", "matrixStats", "matrixTests", "nanoparquet", "qvalue", "reshape2", "rstatix", "spatstat_explore", "spatstat_geom"] }, "Spaniel": { "name": "Spaniel", "version": "1.22.0", "sha256": "0kbl3f5livdy7zjm415nc6ah8g8mdxl7bj7ma491wby3z44h9rlr", "depends": ["DropletUtils", "S4Vectors", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "dplyr", "ggplot2", "igraph", "jpeg", "jsonlite", "magrittr", "png", "scater", "scran", "shiny"] }, "SparseArray": { "name": "SparseArray", "version": "1.8.1", "sha256": "0hkcaqn7nrad6db83pp615bb87yvqiqcw6k3wjhpncrp7s923p8w", "depends": ["BiocGenerics", "IRanges", "Matrix", "MatrixGenerics", "S4Arrays", "S4Vectors", "XVector", "matrixStats"] }, "SparseSignatures": { "name": "SparseSignatures", "version": "2.18.0", "sha256": "00h1i8hy3mkfz7shf00l2jcnkm5fbzlswjydqs6piqg4p2gci33l", "depends": ["BSgenome", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "NMF", "RhpcBLASctl", "data_table", "ggplot2", "gridExtra", "nnlasso", "nnls", "reshape2"] }, "SpatialCPie": { "name": "SpatialCPie", "version": "1.24.0", "sha256": "0pmznha6hqsz685vcw2zpc0cw9g6f3ww2a1pswmfkcn3rj55h0dg", "depends": ["SummarizedExperiment", "colorspace", "data_table", "digest", "dplyr", "ggforce", "ggiraph", "ggplot2", "ggrepel", "igraph", "lpSolve", "purrr", "readr", "rlang", "shiny", "shinyWidgets", "shinycssloaders", "shinyjs", "tibble", "tidyr", "tidyselect", "zeallot"] }, "SpatialDecon": { "name": "SpatialDecon", "version": "1.18.0", "sha256": "1vcwi2njhkwgl46nyn817fycf8hajdc7457wfhs06d7k6dm6a5r5", "depends": ["Biobase", "GeomxTools", "Matrix", "SeuratObject", "logNormReg", "repmis"] }, "SpatialExperiment": { "name": "SpatialExperiment", "version": "1.18.1", "sha256": "0rwdnl46x350s5l0qpv7kfbdbc45yggrwi62dw8s046kbghc9bnz", "depends": ["BiocFileCache", "BiocGenerics", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "magick", "rjson"] }, "SpatialExperimentIO": { "name": "SpatialExperimentIO", "version": "1.0.0", "sha256": "13syrqy7qkblirslrx2k4gikx32imzi97bi0j0j54bccssjrxpgx", "depends": ["DropletUtils", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "arrow", "data_table", "purrr"] }, "SpatialFeatureExperiment": { "name": "SpatialFeatureExperiment", "version": "1.10.1", "sha256": "0l04hwfcphlbn9kw5f9yzqdm8mxxpsnmg11m850jpqfjgw5pgdvf", "depends": ["Biobase", "BiocGenerics", "BiocNeighbors", "BiocParallel", "DropletUtils", "EBImage", "Matrix", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "data_table", "lifecycle", "rjson", "rlang", "sf", "sfheaders", "spatialreg", "spdep", "terra", "zeallot"] }, "SpatialOmicsOverlay": { "name": "SpatialOmicsOverlay", "version": "1.8.0", "sha256": "0dbhml4fybsxdk75nbxk2b39aymgzklki86rp0rz292hk9g8qqs2", "depends": ["Biobase", "BiocFileCache", "EBImage", "GeomxTools", "RBioFormats", "S4Vectors", "XML", "base64enc", "data_table", "dplyr", "ggplot2", "ggtext", "magick", "pbapply", "plotrix", "readxl", "scattermore", "stringr"] }, "SpeCond": { "name": "SpeCond", "version": "1.62.0", "sha256": "190qd4ydczkfckc1b87fm14m0259db53ff65251ygc65z4bw88cb", "depends": ["Biobase", "RColorBrewer", "fields", "hwriter", "mclust"] }, "Spectra": { "name": "Spectra", "version": "1.18.2", "sha256": "0j0d58ypqsrrd2k8zw5mhdhndib40y4sdblj6dgffvy06069wd3r", "depends": ["BiocGenerics", "BiocParallel", "IRanges", "MetaboCoreUtils", "MsCoreUtils", "ProtGenerics", "S4Vectors", "fs"] }, "SpectraQL": { "name": "SpectraQL", "version": "1.2.1", "sha256": "0mk34b4x9azinr887iid8s4zcnzvc3211zrn5z7in5phk9kiq6q8", "depends": ["MsCoreUtils", "ProtGenerics", "Spectra"] }, "SpectralTAD": { "name": "SpectralTAD", "version": "1.24.0", "sha256": "09jm9lm4a0qhk1nz8g98pg2kmm90nnkb9cgd3c8jid6idfnzdgcq", "depends": ["BiocParallel", "GenomicRanges", "HiCcompare", "Matrix", "PRIMME", "cluster", "dplyr", "magrittr"] }, "SpliceWiz": { "name": "SpliceWiz", "version": "1.10.1", "sha256": "1nv7aj6kgsggz3jdvr1kngg5bib0mmjma9ndkvzy7ig22kab5vhx", "depends": ["AnnotationHub", "BSgenome", "BiocFileCache", "BiocGenerics", "BiocParallel", "Biostrings", "DT", "DelayedArray", "DelayedMatrixStats", "GenomeInfoDb", "GenomicRanges", "HDF5Array", "IRanges", "NxtIRFdata", "RColorBrewer", "RSQLite", "R_utils", "Rcpp", "RcppProgress", "S4Vectors", "SummarizedExperiment", "data_table", "fst", "genefilter", "ggplot2", "h5mread", "heatmaply", "htmltools", "httr", "magrittr", "matrixStats", "ompBAM", "patchwork", "pheatmap", "plotly", "progress", "rhandsontable", "rhdf5", "rtracklayer", "rvest", "scales", "shiny", "shinyFiles", "shinyWidgets", "shinydashboard", "stringi"] }, "SplicingFactory": { "name": "SplicingFactory", "version": "1.16.0", "sha256": "1x7c5pkii3f90mcbqmjb9wsbc08c776lb2hbws7hbz4wsg2rdyn5", "depends": ["SummarizedExperiment"] }, "SplicingGraphs": { "name": "SplicingGraphs", "version": "1.48.0", "sha256": "115qvj5zpr2axigr8laar4ja4xz0cjgbl13fki4gkmgckzhm9idl", "depends": ["BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rgraphviz", "Rsamtools", "S4Vectors", "graph", "igraph"] }, "SplineDV": { "name": "SplineDV", "version": "1.0.0", "sha256": "1mwabmbr4jky7zvzqyc6ya79xrpx4cybh2sd927r0jmcxp30s251", "depends": ["Biobase", "BiocGenerics", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "dplyr", "plotly", "scuttle", "sparseMatrixStats"] }, "SpotClean": { "name": "SpotClean", "version": "1.10.0", "sha256": "0dvzbwxg5gw1gkbqh5ddyg6c5yv4wn4a310cdxxdx9m74ra3f58i", "depends": ["Matrix", "RColorBrewer", "S4Vectors", "Seurat", "SpatialExperiment", "SummarizedExperiment", "dplyr", "ggplot2", "readbitmap", "rhdf5", "rjson", "rlang", "tibble", "viridis"] }, "SpotSweeper": { "name": "SpotSweeper", "version": "1.4.0", "sha256": "06q4rh1hxwir0cfyjn6lg6g3h886x0jznglfwnhyr2vlr62k2xhp", "depends": ["BiocNeighbors", "BiocParallel", "MASS", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "escheR", "ggplot2", "spatialEco"] }, "StabMap": { "name": "StabMap", "version": "1.2.0", "sha256": "15nkzvxsf62d12d4cw57z1vxhpdi1ap9i5l086vnwjybdznldg41", "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "MASS", "Matrix", "MatrixGenerics", "SummarizedExperiment", "abind", "igraph", "slam"] }, "Statial": { "name": "Statial", "version": "1.10.0", "sha256": "0nnbqj1qab4dhqzryfq1zq5dbvxpbqy84jl5842k4vb3r2fflrss", "depends": ["BiocParallel", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "cluster", "concaveman", "data_table", "dplyr", "ggplot2", "limma", "magrittr", "plotly", "purrr", "ranger", "spatstat_explore", "spatstat_geom", "stringr", "tibble", "tidyr", "tidyselect", "treekoR"] }, "Streamer": { "name": "Streamer", "version": "1.54.0", "sha256": "0s4l5y0d1pgsf5fy0qz4qw5h95z9vimx95v090f4rzgpwyzn444z", "depends": ["BiocGenerics", "RBGL", "graph"] }, "Structstrings": { "name": "Structstrings", "version": "1.24.0", "sha256": "1hrp77252g5bys6gj7lrqhki8kvsrqpimbyyr7sl6884avim20q2", "depends": ["BiocGenerics", "Biostrings", "IRanges", "S4Vectors", "XVector", "crayon", "stringi", "stringr"] }, "StructuralVariantAnnotation": { "name": "StructuralVariantAnnotation", "version": "1.24.0", "sha256": "0g6h1d5kk499b46dijlvz6nfgx3ihxh3fm97ijnx6k37h5z49md3", "depends": ["BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "assertthat", "dplyr", "pwalign", "rlang", "rtracklayer", "stringr"] }, "SubCellBarCode": { "name": "SubCellBarCode", "version": "1.24.0", "sha256": "0wyiqqc5p3dlp44ljay6mgafjvjwhgdp8d1yrxjg4pwmm363ldb5", "depends": ["AnnotationDbi", "Rtsne", "caret", "e1071", "ggplot2", "ggrepel", "gridExtra", "networkD3", "org_Hs_eg_db", "scatterplot3d"] }, "SummarizedExperiment": { "name": "SummarizedExperiment", "version": "1.38.1", "sha256": "1f48vjcfz3cb1kdsbwjik32z9bbkdmlmlpx895p1v875dxwwlp70", "depends": ["Biobase", "BiocGenerics", "DelayedArray", "GenomeInfoDb", "GenomicRanges", "IRanges", "Matrix", "MatrixGenerics", "S4Arrays", "S4Vectors"] }, "Summix": { "name": "Summix", "version": "2.14.0", "sha256": "1333xp20cfkcrfnna4a86xpba4i8i2npy841yzl851ahydb20avv", "depends": ["BEDASSLE", "dplyr", "magrittr", "nloptr", "randomcoloR", "scales", "tibble", "tidyselect", "visNetwork"] }, "SurfR": { "name": "SurfR", "version": "1.4.1", "sha256": "04yh8ah8198bkp166vsqvi5hcsqkdids39pah6k15n4j22avc2g4", "depends": ["BiocFileCache", "DESeq2", "SPsimSeq", "SummarizedExperiment", "TCGAbiolinks", "assertr", "biomaRt", "curl", "dplyr", "edgeR", "ggplot2", "ggrepel", "gridExtra", "httr", "knitr", "magrittr", "metaRNASeq", "openxlsx", "rhdf5", "rjson", "scales", "stringr", "tidyr", "venn"] }, "SwathXtend": { "name": "SwathXtend", "version": "2.30.0", "sha256": "0z18qg1dc27zylgj9hqxvm2pn5s93r09mc9j3nqc106l5i1iarzp", "depends": ["VennDiagram", "e1071", "lattice", "openxlsx"] }, "SynExtend": { "name": "SynExtend", "version": "1.20.2", "sha256": "0qc45qnsmn4mcybhamx4hd4jkr81fy7m5l74b6ssxkqhzgjq69sk", "depends": ["Biostrings", "DBI", "DECIPHER", "IRanges", "RSQLite", "S4Vectors"] }, "SynMut": { "name": "SynMut", "version": "1.24.0", "sha256": "08f1lyvpfqy1268s6j2j9bf0lb4w3b32rc8i6j0mi0j9m3kzsfxf", "depends": ["BiocGenerics", "Biostrings", "seqinr", "stringr"] }, "TADCompare": { "name": "TADCompare", "version": "1.18.0", "sha256": "0mc1rf56p5xyycn4rp73jfv46gi6vbgbd562ccvhkj0mb124xajl", "depends": ["HiCcompare", "Matrix", "PRIMME", "RColorBrewer", "cluster", "cowplot", "dplyr", "ggplot2", "ggpubr", "magrittr", "reshape2", "tidyr"] }, "TAPseq": { "name": "TAPseq", "version": "1.20.0", "sha256": "1p19mx3zipdrk5nmlsa8lc55rrrgdca4jflk1bhf4c0plviympz1", "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "dplyr", "tidyr"] }, "TBSignatureProfiler": { "name": "TBSignatureProfiler", "version": "1.20.0", "sha256": "1k6hzklr16rh3fn79q1cskzvnwlq3sxmsymslra4bgyq9kik6bcv", "depends": ["ASSIGN", "BiocParallel", "ComplexHeatmap", "DESeq2", "DT", "GSVA", "HGNChelper", "RColorBrewer", "ROCit", "S4Vectors", "SummarizedExperiment", "edgeR", "gdata", "ggplot2", "glmnet", "magrittr", "pROC", "reshape2", "singscore", "tibble"] }, "TCC": { "name": "TCC", "version": "1.48.0", "sha256": "1f627k01p47rh6f8isba6ydwvsg28xr1n6zharnp5z4m0hiapf5w", "depends": ["DESeq2", "ROC", "edgeR"] }, "TCGAbiolinks": { "name": "TCGAbiolinks", "version": "2.36.0", "sha256": "1ahpj0609x2wa2rzvkfdaia6026flh011lg53lrnagxh1wi55qkc", "depends": ["GenomicRanges", "IRanges", "R_utils", "S4Vectors", "SummarizedExperiment", "TCGAbiolinksGUI_data", "XML", "biomaRt", "data_table", "downloader", "dplyr", "ggplot2", "httr", "jsonlite", "knitr", "plyr", "purrr", "readr", "rvest", "stringr", "tibble", "tidyr", "xml2"] }, "TCGAutils": { "name": "TCGAutils", "version": "1.28.0", "sha256": "1jkqmla4wr1dg78g29clhb0vljmyhlz8ad2wm8acs6gx4irbdxg0", "depends": ["AnnotationDbi", "BiocBaseUtils", "BiocGenerics", "GenomeInfoDb", "GenomicDataCommons", "GenomicFeatures", "GenomicRanges", "IRanges", "MultiAssayExperiment", "RaggedExperiment", "S4Vectors", "SummarizedExperiment", "rvest", "stringr", "xml2"] }, "TCseq": { "name": "TCseq", "version": "1.32.0", "sha256": "0n3w1dgpqfyq6gkdc5cqx7p6srb1pjfwq66rn32956wja43v9q1x", "depends": ["BiocGenerics", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "SummarizedExperiment", "cluster", "e1071", "edgeR", "ggplot2", "locfit", "reshape2"] }, "TDbasedUFE": { "name": "TDbasedUFE", "version": "1.8.0", "sha256": "17y5yi0x168ma9b33fhkykc1w94y394r5l716rfqr8s9iqsddmf2", "depends": ["GenomicRanges", "MOFAdata", "rTensor", "readr", "shiny", "tximport", "tximportData"] }, "TDbasedUFEadv": { "name": "TDbasedUFEadv", "version": "1.8.1", "sha256": "01k0candqvkshpf6sc886c37481hh39b25ik67pvy7hqh8rg6h4r", "depends": ["Biobase", "DOSE", "GenomicRanges", "RTCGA", "STRINGdb", "TDbasedUFE", "enrichR", "enrichplot", "hash", "rTensor", "shiny"] }, "TEKRABber": { "name": "TEKRABber", "version": "1.12.0", "sha256": "1nbisldzrxadw86nffarrcnkyrhs76qsfimsx2mhj98dcv7190ig", "depends": ["DESeq2", "GenomeInfoDb", "Rcpp", "SCBN", "apeglm", "biomaRt", "doParallel", "dplyr", "foreach", "magrittr", "rtracklayer"] }, "TENET": { "name": "TENET", "version": "1.0.1", "sha256": "03rrsld0rk40c6qyq5wpdq8dflhcx1hgs2svdlxjnxqa6dhyvqzh", "depends": ["AnnotationHub", "BSgenome_Hsapiens_UCSC_hg38", "Biostrings", "ExperimentHub", "GenomicRanges", "IRanges", "MultiAssayExperiment", "RCircos", "R_utils", "S4Vectors", "SummarizedExperiment", "TCGAbiolinks", "TENET_ExperimentHub", "ggplot2", "matlab", "pastecs", "rtracklayer", "seqLogo", "sesame", "sesameData", "survival"] }, "TENxIO": { "name": "TENxIO", "version": "1.10.2", "sha256": "0bmvwp3ji15i044c4x6y4cslaxq5glwar0a0662c121m9m7kbffb", "depends": ["BiocBaseUtils", "BiocGenerics", "BiocIO", "GenomeInfoDb", "GenomicRanges", "HDF5Array", "Matrix", "MatrixGenerics", "RCurl", "R_utils", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "readr", "rhdf5"] }, "TEQC": { "name": "TEQC", "version": "4.30.0", "sha256": "0mm33s75i527h8q3p4sdxmrcwh4xcr6lff3334719mh296gfgqja", "depends": ["Biobase", "BiocGenerics", "IRanges", "Rsamtools", "hwriter"] }, "TFARM": { "name": "TFARM", "version": "1.30.0", "sha256": "11qrxlcwdkhnqgki4b47dpc0zcv1w7scmprjiy84afid9kyykfp9", "depends": ["GenomicRanges", "arules", "fields", "gplots", "stringr"] }, "TFBSTools": { "name": "TFBSTools", "version": "1.46.0", "sha256": "149bhv3h8d5lr17l7bndjpmp0g48yp07kiankwvqkrl2zilr17kk", "depends": ["BSgenome", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "DBI", "DirichletMultinomial", "GenomeInfoDb", "GenomicRanges", "IRanges", "RSQLite", "S4Vectors", "TFMPvalue", "XML", "XVector", "caTools", "gtools", "pwalign", "rtracklayer", "seqLogo"] }, "TFEA_ChIP": { "name": "TFEA.ChIP", "version": "1.28.0", "sha256": "1pwf4gxxls9mzbzm7crnhw01pajl3plbh1fm6qaz4m5ra9b7wkq2", "depends": ["GenomicFeatures", "GenomicRanges", "IRanges", "R_utils", "biomaRt", "dplyr", "org_Hs_eg_db"] }, "TFHAZ": { "name": "TFHAZ", "version": "1.30.0", "sha256": "0hl6wmbkaq9g7imhh95sqz832ccq524hax1j5vrypgbxcvk73vgv", "depends": ["GenomicRanges", "IRanges", "ORFik", "S4Vectors"] }, "TFutils": { "name": "TFutils", "version": "1.28.0", "sha256": "1ciwf64gia2fn7xxxksjf4kg9996yx9zfjn0fk0xlrjaj8ald4ps", "depends": ["AnnotationDbi", "BiocFileCache", "DT", "GSEABase", "GenomicFiles", "Rsamtools", "SummarizedExperiment", "dplyr", "httr", "magrittr", "miniUI", "org_Hs_eg_db", "readxl", "rjson", "shiny"] }, "TIN": { "name": "TIN", "version": "1.40.0", "sha256": "063j4axil7yy1b555jhq36d2v6lsw4ar53vkghyb0hh1j9yhgcw6", "depends": ["WGCNA", "aroma_affymetrix", "data_table", "impute", "squash", "stringr"] }, "TMSig": { "name": "TMSig", "version": "1.2.0", "sha256": "165xbvn61l8zxlywdczx1r0sakhq956qdhxjk73ixq486qz9zn16", "depends": ["ComplexHeatmap", "GSEABase", "Matrix", "circlize", "data_table", "limma"] }, "TMixClust": { "name": "TMixClust", "version": "1.30.0", "sha256": "06bk1h4ngxgaws27n8yd6pqp730gwimnvqq9acmvkxwh35yph9ab", "depends": ["Biobase", "BiocParallel", "SPEM", "cluster", "flexclust", "gss", "mvtnorm", "zoo"] }, "TOAST": { "name": "TOAST", "version": "1.22.0", "sha256": "0zi8j5g4gifg40yhr6z0ip7xkrivd8b0hjsg8ik6i258n2dn9100", "depends": ["EpiDISH", "GGally", "SummarizedExperiment", "corpcor", "doParallel", "ggplot2", "limma", "nnls", "quadprog", "tidyr"] }, "TOP": { "name": "TOP", "version": "1.8.0", "sha256": "1g7ghaw2diq3p7l985rid1yi8lgpig4pdj2m0a9bnp6ri22lxfr0", "depends": ["ClassifyR", "Hmisc", "assertthat", "caret", "directPA", "doParallel", "dplyr", "ggnewscale", "ggplot2", "ggraph", "ggrepel", "ggthemes", "glmnet", "igraph", "latex2exp", "limma", "magrittr", "pROC", "plotly", "purrr", "reshape2", "statmod", "stringr", "survival", "tibble", "tidygraph", "tidyr"] }, "TPP": { "name": "TPP", "version": "3.36.0", "sha256": "0mkwp5q0qm9cp7wwsnxy55ljrgkzxxzsf51yfr7428w33mmwwq2b", "depends": ["Biobase", "MASS", "RColorBrewer", "RCurl", "VGAM", "VennDiagram", "biobroom", "broom", "data_table", "doParallel", "dplyr", "foreach", "futile_logger", "ggplot2", "gridExtra", "knitr", "limma", "magrittr", "mefa", "nls2", "openxlsx", "plyr", "purrr", "reshape2", "rmarkdown", "stringr", "tibble", "tidyr"] }, "TPP2D": { "name": "TPP2D", "version": "1.24.0", "sha256": "0yf7g0yzh9hidk6qdp47y0263l2mn710zj0fw32j0ynjlm96m5l4", "depends": ["BiocParallel", "MASS", "RCurl", "doParallel", "dplyr", "foreach", "ggplot2", "limma", "openxlsx", "stringr", "tidyr"] }, "TREG": { "name": "TREG", "version": "1.12.0", "sha256": "14yl6vxnrajmqh7nrpaa2nmyq8713rnkgq7b53vd9mxpb4plfv1f", "depends": ["Matrix", "SummarizedExperiment", "purrr", "rafalib"] }, "TRESS": { "name": "TRESS", "version": "1.14.0", "sha256": "1hc755ng31ks1sxndg3lmr8faif5rcqdi17fvwi21x2cjy88msxy", "depends": ["AnnotationDbi", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "Rsamtools", "S4Vectors", "matrixStats", "rtracklayer"] }, "TRONCO": { "name": "TRONCO", "version": "2.40.0", "sha256": "0il19f229glhim96sr6h1h31lkg86ancmqfr9r4gfkbmwf6lmnh5", "depends": ["RColorBrewer", "R_matlab", "Rgraphviz", "bnlearn", "circlize", "doParallel", "foreach", "gridExtra", "gtable", "gtools", "igraph", "iterators", "scales", "xtable"] }, "TSAR": { "name": "TSAR", "version": "1.6.0", "sha256": "1ng2l4k8wx8s4i2w16fv2b0pl5c95whx63ybmmva4l7abyrx5k0p", "depends": ["dplyr", "ggplot2", "ggpubr", "jsonlite", "magrittr", "mgcv", "minpack_lm", "openxlsx", "plotly", "readxl", "rhandsontable", "shiny", "shinyWidgets", "shinyjs", "stringr", "tidyr"] }, "TSCAN": { "name": "TSCAN", "version": "1.46.0", "sha256": "1xn3wvrsydqyjd7nq8a3iz079ci25cv16zvx2s9gn9mjpcjw3hl6", "depends": ["DelayedArray", "Matrix", "S4Vectors", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "TrajectoryUtils", "combinat", "fastICA", "ggplot2", "gplots", "igraph", "mclust", "mgcv", "plyr", "shiny"] }, "TTMap": { "name": "TTMap", "version": "1.30.0", "sha256": "1f3klkw9gy1f70dvpvgjrc4f1iq2001s22m57yr5g0d0vi9aprf0", "depends": ["Biobase", "SummarizedExperiment", "colorRamps", "rgl"] }, "TVTB": { "name": "TVTB", "version": "1.34.1", "sha256": "1w4ki0qrwk8sw5dy3020rqx8g2kymb4a17jlzl3wnadpsnn072zj", "depends": ["AnnotationFilter", "BiocGenerics", "BiocParallel", "Biostrings", "GGally", "GenomeInfoDb", "GenomicRanges", "Gviz", "IRanges", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "ensembldb", "ggplot2", "limma", "reshape2"] }, "TargetDecoy": { "name": "TargetDecoy", "version": "1.14.0", "sha256": "15l5adc20m4pf77ywifzm3m3yavm59nxjbk3kh51brj6s0y97k0x", "depends": ["ggplot2", "ggpubr", "miniUI", "mzID", "mzR", "shiny"] }, "TargetScore": { "name": "TargetScore", "version": "1.46.0", "sha256": "1m1p9n3h7gsbln061fcnjynz4p8k97vwfnj7bz90v8608d456lbm", "depends": ["Matrix", "pracma"] }, "TargetSearch": { "name": "TargetSearch", "version": "2.10.0", "sha256": "0iq9yhx897igc9gimkf7ig6116bk9rzvrh0v0sp8n9z3r79khzw9", "depends": ["assertthat", "ncdf4"] }, "TaxSEA": { "name": "TaxSEA", "version": "1.0.0", "sha256": "1vhilxjfprbxl6vrms6ar4fm0pr1v3bydfwpwb1vgvh23wy3mvrr", "depends": [] }, "TileDBArray": { "name": "TileDBArray", "version": "1.18.0", "sha256": "1l7hgy39szsslzxi2hmhi5764l39a1jx1sh0xickbyawjn1jp442", "depends": ["DelayedArray", "S4Vectors", "SparseArray", "tiledb"] }, "TissueEnrich": { "name": "TissueEnrich", "version": "1.28.0", "sha256": "0b8claj69x94k79mgvy6jw2iz3axl9nkdh27vljsv29gw7lf2vyh", "depends": ["GSEABase", "SummarizedExperiment", "dplyr", "ggplot2", "tidyr"] }, "TitanCNA": { "name": "TitanCNA", "version": "1.45.0", "sha256": "19znhy9gd40fcv3m1zx6kdh178f74j88rb5pkrdv53q48vcq68l3", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "VariantAnnotation", "data_table", "dplyr", "foreach"] }, "TnT": { "name": "TnT", "version": "1.30.0", "sha256": "1f8790i64qlbl6kjyfq971vyjppx56qavrm8fh0hykp36f21swzs", "depends": ["Biobase", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "data_table", "htmlwidgets", "jsonlite", "knitr"] }, "ToxicoGx": { "name": "ToxicoGx", "version": "2.12.0", "sha256": "072xin3r4hwbgln4qyj1w1by9w6vbjfn3fy1g6jpzhq9b6czj7m1", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "CoreGx", "S4Vectors", "SummarizedExperiment", "assertthat", "caTools", "data_table", "downloader", "dplyr", "ggplot2", "jsonlite", "limma", "magrittr", "reshape2", "scales", "tibble", "tidyr"] }, "TrIdent": { "name": "TrIdent", "version": "1.0.0", "sha256": "1pp5qm058k1kz03prq2072nwnzncxb6akwq005bj358v3k0gjlsn", "depends": ["dplyr", "ggplot2", "patchwork", "roll", "stringr", "tidyr"] }, "TrajectoryGeometry": { "name": "TrajectoryGeometry", "version": "1.16.0", "sha256": "0k639jwadjz9kg7l7cc5i30xc24dz456kn7y6d66b2w92ad0zvds", "depends": ["ggplot2", "pracma", "rgl"] }, "TrajectoryUtils": { "name": "TrajectoryUtils", "version": "1.16.1", "sha256": "0p8i8ah8dclir7wqpqcszy811kla397w2876q03j4vpwhp4f5r8f", "depends": ["Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "igraph"] }, "TreeAndLeaf": { "name": "TreeAndLeaf", "version": "1.20.0", "sha256": "12jg75hh8ldvcx6yp5ml9l4dps0y297za9v7snpqp5aj88aszxz8", "depends": ["RedeR", "ape", "igraph"] }, "TreeSummarizedExperiment": { "name": "TreeSummarizedExperiment", "version": "2.16.1", "sha256": "0x2jwvp5ljax9ll1sd7fpnxfzkyh3zacz4566qln1iaapis0w1dq", "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "IRanges", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "ape", "dplyr", "rlang", "treeio"] }, "Trendy": { "name": "Trendy", "version": "1.30.0", "sha256": "0b7crg1hw4kl0rizwivpzvbj5q0i7mz3kih5x6r01qdxg9a17v95", "depends": ["BiocParallel", "DT", "S4Vectors", "SummarizedExperiment", "gplots", "magrittr", "segmented", "shiny", "shinyFiles"] }, "TurboNorm": { "name": "TurboNorm", "version": "1.56.0", "sha256": "14lnlmasfhbybmnxnrdvksihgilk8qv5c86pkpl0is3a8jjgcb7b", "depends": ["affy", "convert", "lattice", "limma", "marray"] }, "UCSC_utils": { "name": "UCSC.utils", "version": "1.4.0", "sha256": "09hs7p43b4p7yif427v4jp10c43im6sqfm4hhfbi38llib7q09nv", "depends": ["S4Vectors", "httr", "jsonlite"] }, "UCell": { "name": "UCell", "version": "2.12.0", "sha256": "0s4i76ar2igg6jfas4a8l801ma914kvk4qx3sz8f5l3j73yjishx", "depends": ["BiocNeighbors", "BiocParallel", "Matrix", "SingleCellExperiment", "SummarizedExperiment", "data_table"] }, "UMI4Cats": { "name": "UMI4Cats", "version": "1.18.1", "sha256": "09pqabcinqis4liq2i6ra5m6y01vl77zami05ziivhq8x13i6s64", "depends": ["BSgenome", "BiocFileCache", "BiocGenerics", "Biostrings", "DESeq2", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "RColorBrewer", "R_utils", "Rbowtie2", "Rsamtools", "S4Vectors", "ShortRead", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg19_knownGene", "annotate", "cowplot", "dplyr", "fda", "ggplot2", "magick", "magrittr", "org_Hs_eg_db", "rappdirs", "regioneR", "reshape2", "rlang", "scales", "stringr", "zoo"] }, "UNDO": { "name": "UNDO", "version": "1.50.0", "sha256": "190j8khw7dc7axk656cvdl7qqc0i5rxyx6h5wp1hbw1zz8xq4vx0", "depends": ["Biobase", "BiocGenerics", "MASS", "boot", "nnls"] }, "UPDhmm": { "name": "UPDhmm", "version": "1.4.0", "sha256": "0iq3fa1scqgh91b6vrn39156vsfvfdzhak36a39zd72v1c7xznhi", "depends": ["GenomicRanges", "HMM", "IRanges", "S4Vectors", "VariantAnnotation"] }, "Ularcirc": { "name": "Ularcirc", "version": "1.26.0", "sha256": "1sshb36x9vnqfc2bbya1ikpy44arz19a3dmcbqwnbf6al7xfcpmx", "depends": ["AnnotationDbi", "AnnotationHub", "BSgenome", "BiocGenerics", "Biostrings", "DT", "GenomeInfoDb", "GenomeInfoDbData", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Organism_dplyr", "R_utils", "S4Vectors", "data_table", "ggplot2", "ggrepel", "gsubfn", "mirbase_db", "moments", "plotgardener", "shiny", "shinyFiles", "shinydashboard", "shinyjs", "yaml"] }, "UniProt_ws": { "name": "UniProt.ws", "version": "2.48.0", "sha256": "17yzrwkr3126zc56pq4kxd36jfklm515sd6l8qx0x2s0n5q44gch", "depends": ["AnVILBase", "AnnotationDbi", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "httr2", "jsonlite", "progress", "rjsoncons"] }, "Uniquorn": { "name": "Uniquorn", "version": "2.28.0", "sha256": "01ynlr38hwxvwa93miqyr7f1idr8aanhcn48mqq1jfgzzwn860a6", "depends": ["GenomicRanges", "IRanges", "R_utils", "VariantAnnotation", "WriteXLS", "data_table", "doParallel", "foreach", "stringr"] }, "VAExprs": { "name": "VAExprs", "version": "1.14.0", "sha256": "1g4n28m54kmswfqklfkv8ssdqzfzywv7vwjkglf74z98plymhrc0", "depends": ["CatEncoders", "DeepPINCS", "DiagrammeR", "SingleCellExperiment", "SummarizedExperiment", "keras", "mclust", "purrr", "scater", "tensorflow"] }, "VCFArray": { "name": "VCFArray", "version": "1.24.0", "sha256": "1az9sk8xydmpqlb3xcv5df11gpmcy1b12nq33svka1h0gxi1ynlj", "depends": ["BiocGenerics", "DelayedArray", "GenomicFiles", "GenomicRanges", "Rsamtools", "S4Vectors", "VariantAnnotation"] }, "VDJdive": { "name": "VDJdive", "version": "1.10.0", "sha256": "102ldkmabxw755y32yxba6604a61gxlsrn5a1zpk8qh4l54zpvj6", "depends": ["BiocParallel", "IRanges", "Matrix", "RColorBrewer", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "cowplot", "ggplot2", "gridExtra"] }, "VERSO": { "name": "VERSO", "version": "1.18.0", "sha256": "0ldn8ahzy1wlsx2jly2vkcvkgknzqmh7mb573rzk05m9fpaaym7l", "depends": ["Rfast", "ape", "data_tree"] }, "VaSP": { "name": "VaSP", "version": "1.20.0", "sha256": "0d7rn0v0w5a71703ivw590f93qaa7720zpa9zaqzy24bg4nh19gn", "depends": ["GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "ballgown", "cluster", "matrixStats"] }, "VanillaICE": { "name": "VanillaICE", "version": "1.70.1", "sha256": "0d2r25msysal3142gn804hmmr2pbwrsy508l5znqgh2wvzpynnk6", "depends": ["BSgenome_Hsapiens_UCSC_hg18", "Biobase", "BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "MatrixGenerics", "S4Vectors", "SummarizedExperiment", "crlmm", "data_table", "foreach", "lattice", "matrixStats", "oligoClasses"] }, "VarCon": { "name": "VarCon", "version": "1.16.0", "sha256": "0ssv561x3ippngwc64s1drf4ls7r93c082klkr2ayly1wp93kcyn", "depends": ["BSgenome", "Biostrings", "GenomicRanges", "IRanges", "ggplot2", "shiny", "shinyFiles", "shinycssloaders"] }, "VariantAnnotation": { "name": "VariantAnnotation", "version": "1.54.1", "sha256": "0w4k79azyb3s8m1spcmqjmzx3ig9mnzv5vnlcfaxk0p8z0ahzxfr", "depends": ["AnnotationDbi", "BSgenome", "Biobase", "BiocGenerics", "Biostrings", "DBI", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "MatrixGenerics", "Rhtslib", "Rsamtools", "S4Vectors", "SummarizedExperiment", "XVector", "rtracklayer"] }, "VariantExperiment": { "name": "VariantExperiment", "version": "1.22.0", "sha256": "112w5sqkvx4vi50z9n6h2xxjrh4ir9n35k3zybvxmv0glksamizg", "depends": ["Biostrings", "DelayedArray", "DelayedDataFrame", "GDSArray", "GenomicRanges", "IRanges", "S4Vectors", "SNPRelate", "SeqArray", "SummarizedExperiment", "gdsfmt"] }, "VariantFiltering": { "name": "VariantFiltering", "version": "1.44.0", "sha256": "124d1zn0ap1kfc8f1ks8rr392dsks3h4qr6i9pkkz1q8s9mk420b", "depends": ["AnnotationDbi", "BSgenome", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "DT", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "GenomicScores", "Gviz", "IRanges", "RBGL", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "XVector", "graph", "shiny", "shinyTree", "shinyjs", "shinythemes"] }, "VariantTools": { "name": "VariantTools", "version": "1.50.0", "sha256": "03x4q4siz32fcljzvxdvz58zly11pnvycv65kbzam1nb9vg312v2", "depends": ["BSgenome", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "Rsamtools", "S4Vectors", "VariantAnnotation", "rtracklayer"] }, "VegaMC": { "name": "VegaMC", "version": "3.46.0", "sha256": "0xxbpynwgaywrgkazd97shkk34yl3skhgbms1vxgypgrzhhhhiag", "depends": ["Biobase", "biomaRt"] }, "VennDetail": { "name": "VennDetail", "version": "1.23.0", "sha256": "0c64dk2w4azavz2b9455gilimxnmng0ix02bksl4j99868wdfhgh", "depends": ["UpSetR", "VennDiagram", "dplyr", "futile_logger", "ggplot2", "magrittr", "purrr", "tibble"] }, "ViSEAGO": { "name": "ViSEAGO", "version": "1.22.0", "sha256": "0hwaq9zlyfrb5yc10i4kbfxgq06b2272b0mb17smd5cmax3i336g", "depends": ["AnnotationDbi", "AnnotationForge", "ComplexHeatmap", "DT", "DiagrammeR", "GOSemSim", "GO_db", "RColorBrewer", "R_utils", "UpSetR", "biomaRt", "circlize", "data_table", "dendextend", "dynamicTreeCut", "fgsea", "ggplot2", "heatmaply", "htmlwidgets", "igraph", "plotly", "scales", "topGO"] }, "VisiumIO": { "name": "VisiumIO", "version": "1.4.3", "sha256": "0j9yf2n8lvgygkb6l79n4yz64wl1bran1hdpjfggivccpi0c8icv", "depends": ["BiocBaseUtils", "BiocGenerics", "BiocIO", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "TENxIO", "jsonlite"] }, "Voyager": { "name": "Voyager", "version": "1.10.0", "sha256": "0q4bk4vgaxynrj2vqdlwv187fplxm86g5myizfwvb6s52q85d039", "depends": ["BiocParallel", "DelayedArray", "Matrix", "MatrixGenerics", "RSpectra", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SpatialFeatureExperiment", "SummarizedExperiment", "bluster", "ggnewscale", "ggplot2", "lifecycle", "memuse", "patchwork", "rlang", "scales", "scico", "sf", "spdep", "terra", "zeallot"] }, "VplotR": { "name": "VplotR", "version": "1.18.0", "sha256": "01qs6cnbb4vb3z5al2irgllg3xk3g6vy4ymb4jjybaz0kykbn8bn", "depends": ["GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "cowplot", "ggplot2", "magrittr", "reshape2", "zoo"] }, "Wrench": { "name": "Wrench", "version": "1.26.0", "sha256": "13487bw2330g5vsj3qx3kff2h9b1qzb81gx15qsdmpbrgp00n5dg", "depends": ["limma", "locfit", "matrixStats"] }, "XAItest": { "name": "XAItest", "version": "1.0.1", "sha256": "0i9ks1p3l354pxr9s3k0kjs6b064q9ff7w0qf09prn8cxkivpfig", "depends": ["DT", "SummarizedExperiment", "caret", "ggplot2", "kernelshap", "lime", "limma", "randomForest"] }, "XDE": { "name": "XDE", "version": "2.54.0", "sha256": "127s5y121g2x669mcmyvvx5qxbzp8nsqcda1gkfjskbmwi7lhycf", "depends": ["Biobase", "BiocGenerics", "GeneMeta", "RColorBrewer", "genefilter", "gtools", "mvtnorm", "siggenes"] }, "XINA": { "name": "XINA", "version": "1.26.0", "sha256": "0nyasz6bn7qkxayihbh26qdmzmw716sqbwzysr17p24p3bzs5rhl", "depends": ["STRINGdb", "alluvial", "ggplot2", "gridExtra", "igraph", "mclust", "plyr"] }, "XNAString": { "name": "XNAString", "version": "1.15.0", "sha256": "1q50h6fvkc8fr5kvz3whvfiqx3fkxi8m7r1h459sqk362j9pydrj", "depends": ["BSgenome", "Biostrings", "GenomicRanges", "IRanges", "Rcpp", "S4Vectors", "data_table", "formattable", "future_apply", "pwalign", "stringi", "stringr"] }, "XVector": { "name": "XVector", "version": "0.48.0", "sha256": "0mwv82k50jmqgmjwdlsjk5pviszvblidg3447g5381zj8489g9r3", "depends": ["BiocGenerics", "IRanges", "S4Vectors"] }, "XeniumIO": { "name": "XeniumIO", "version": "1.0.0", "sha256": "0yd0kf34dw3lyphvlqhw1h6b0qcyfq86lg4455mqvklx96vpvm3c", "depends": ["BiocBaseUtils", "BiocGenerics", "BiocIO", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "TENxIO", "VisiumIO", "jsonlite"] }, "Xeva": { "name": "Xeva", "version": "1.24.0", "sha256": "1f3jlk8827r1pq4aj7bkqla0i05f6qn4bya8gxxqghdby5nkphhp", "depends": ["BBmisc", "Biobase", "ComplexHeatmap", "PharmacoGx", "Rmisc", "doParallel", "downloader", "ggplot2", "nlme", "scales"] }, "YAPSA": { "name": "YAPSA", "version": "1.34.0", "sha256": "1i8n46ifxbhnngqk4qb93mxj07ngzr43759mw58kf0j73xp5vx4b", "depends": ["BSgenome_Hsapiens_UCSC_hg19", "Biostrings", "ComplexHeatmap", "GenomeInfoDb", "GenomicRanges", "GetoptLong", "KEGGREST", "PMCMRplus", "SomaticSignatures", "VariantAnnotation", "circlize", "corrplot", "dendextend", "doParallel", "dplyr", "ggbeeswarm", "ggplot2", "gridExtra", "gtrellis", "limSolve", "magrittr", "pracma", "reshape2"] }, "ZygosityPredictor": { "name": "ZygosityPredictor", "version": "1.8.0", "sha256": "1ain9yvg80vw3av9izqb6my3pqsgp7cqmdcjgq7a3rdw1jwngv33", "depends": ["DelayedArray", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "VariantAnnotation", "dplyr", "igraph", "knitr", "magrittr", "purrr", "readr", "rlang", "stringr", "tibble"] }, "a4": { "name": "a4", "version": "1.56.0", "sha256": "0x43160m0slxpfqv3irdg56j6l1vrvj1lllh9iwrgp3m0mvsysab", "depends": ["a4Base", "a4Classif", "a4Core", "a4Preproc", "a4Reporting"] }, "a4Base": { "name": "a4Base", "version": "1.56.0", "sha256": "077cmq1m0mwjlpyxb3wa9z1j1cfagvj1c116y90izvznb1pmsf7s", "depends": ["Biobase", "a4Core", "a4Preproc", "annaffy", "genefilter", "glmnet", "gplots", "limma", "mpm", "multtest"] }, "a4Classif": { "name": "a4Classif", "version": "1.56.0", "sha256": "0yk5ww3f90fyy3jd2p93560708ii66sxij3mfqxpi0012mqlhlkh", "depends": ["Biobase", "ROCR", "a4Core", "a4Preproc", "glmnet", "pamr", "varSelRF"] }, "a4Core": { "name": "a4Core", "version": "1.56.0", "sha256": "0mwkgw34z5smnrj38jn1vlbicxv4xy799dgr4nxbpcydnn5xlhxf", "depends": ["Biobase", "glmnet"] }, "a4Preproc": { "name": "a4Preproc", "version": "1.56.0", "sha256": "01z9yr9syn6yfndc4vk2cfkc2kgfabpp1fq0liivglpdyzjg0mk2", "depends": ["Biobase", "BiocGenerics"] }, "a4Reporting": { "name": "a4Reporting", "version": "1.56.0", "sha256": "0akwk8l3d49qx5prs7l4zyyjx55vja7v4gmv3drxgcg5782f7923", "depends": ["xtable"] }, "aCGH": { "name": "aCGH", "version": "1.86.0", "sha256": "0md1dpwvhpmb21j2l0n5vkc7k0iw1mviksja0yxmwpjvcbhdwg7v", "depends": ["Biobase", "cluster", "multtest", "survival"] }, "abseqR": { "name": "abseqR", "version": "1.26.0", "sha256": "09d1jd35q6sc5f807hlc65nmglyv34zsicciwbr4s80dgn6i0qih", "depends": ["BiocParallel", "BiocStyle", "RColorBrewer", "VennDiagram", "circlize", "flexdashboard", "ggcorrplot", "ggdendro", "ggplot2", "gridExtra", "knitr", "plotly", "plyr", "png", "reshape2", "rmarkdown", "stringr", "vegan"] }, "acde": { "name": "acde", "version": "1.38.0", "sha256": "1zns18s5mcqlqcnjfhgppayilnpg2b14rmm76phq1a9zbxn7i8yg", "depends": ["boot"] }, "adSplit": { "name": "adSplit", "version": "1.78.0", "sha256": "1lan9m80596c8fawyn1s1dz9bbcaggl726yigssycbkhpdla2yzv", "depends": ["AnnotationDbi", "Biobase", "GO_db", "KEGGREST", "cluster", "multtest"] }, "adductomicsR": { "name": "adductomicsR", "version": "1.24.0", "sha256": "02xzzp42m3zamys2xag2j3n5l7g7viig53alrswvflcscb8qjzcy", "depends": ["AnnotationHub", "DT", "ExperimentHub", "OrgMassSpecR", "RcppEigen", "adductData", "ade4", "bootstrap", "data_table", "doSNOW", "dplyr", "fastcluster", "foreach", "fpc", "mzR", "pastecs", "pracma", "reshape2", "rvest", "smoother", "zoo"] }, "adverSCarial": { "name": "adverSCarial", "version": "1.6.0", "sha256": "14jd37klw8xzfb7fbvaqj5jyc8dy2p0cwc1hyl239p8yjxqindkr", "depends": ["DelayedArray", "S4Vectors", "gtools"] }, "affxparser": { "name": "affxparser", "version": "1.80.0", "sha256": "1j3l2i2z23rsayr0g2wzyp31vpb7h027jmjz8cbx8hnnapwyd36f", "depends": [] }, "affy": { "name": "affy", "version": "1.86.0", "sha256": "0pk7wvqk5xzlnwly7sbpij3waypwlnrli0bnxvjhbrlgc3pnks4g", "depends": ["Biobase", "BiocGenerics", "BiocManager", "affyio", "preprocessCore"] }, "affyContam": { "name": "affyContam", "version": "1.66.0", "sha256": "1r3zhfpzb65h4l92bij06z7k9kidmd7c6i2815mb22975x5hg66z", "depends": ["Biobase", "affy", "affydata"] }, "affyILM": { "name": "affyILM", "version": "1.60.0", "sha256": "0bf9hl0afv9zm1vskqiszzqb3lpqz8yzjw74dyw7739j4p0gfqn8", "depends": ["Biobase", "affxparser", "affy", "gcrma"] }, "affyPLM": { "name": "affyPLM", "version": "1.84.0", "sha256": "0lhin8wn2jh7p5rfgbnz84xjr7xhvks1qlnfj078aypk2b8di1hl", "depends": ["Biobase", "BiocGenerics", "affy", "gcrma", "preprocessCore"] }, "affycomp": { "name": "affycomp", "version": "1.84.0", "sha256": "10xcsbiwbkhyfxjp4xkxi6fbrj10m1v2isl2m5frcqcffjw2ss41", "depends": ["Biobase"] }, "affycoretools": { "name": "affycoretools", "version": "1.80.0", "sha256": "06ajyglz4sida0vqnmlknga4kb3gv626j5ky0lfw0y1y73kjk19i", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "DBI", "GOstats", "Glimma", "RSQLite", "ReportingTools", "S4Vectors", "affy", "edgeR", "gcrma", "ggplot2", "gplots", "hwriter", "lattice", "limma", "oligoClasses", "xtable"] }, "affyio": { "name": "affyio", "version": "1.78.0", "sha256": "1j3r28m0daxlbysyajwhyl6j1vcy4mbq951yyh2j1c8b4jnncf9i", "depends": [] }, "affylmGUI": { "name": "affylmGUI", "version": "1.82.0", "sha256": "0lpf71axddzvlji2sbf4jrjzh7lxyxf017w5wnr0ccnxa34pdm3j", "depends": ["AnnotationDbi", "BiocGenerics", "BiocManager", "R2HTML", "affy", "affyPLM", "affyio", "gcrma", "limma", "tkrplot", "xtable"] }, "aggregateBioVar": { "name": "aggregateBioVar", "version": "1.18.0", "sha256": "0db183h2vb4f8j7rjvs3hm6xnv0k52313m63hxk9ap4n8k140yis", "depends": ["Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "rlang", "tibble"] }, "agilp": { "name": "agilp", "version": "3.40.0", "sha256": "0xvg8fbvp0rb015pvlry8v81kdjmikw47lajfmpvkpirsdl4dp51", "depends": [] }, "airpart": { "name": "airpart", "version": "1.16.0", "sha256": "0hsqzzx800py6j95c9mbf212nyki0fhxbjlwj51giarnnfsghl1r", "depends": ["ComplexHeatmap", "RColorBrewer", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "apeglm", "clue", "dplyr", "dynamicTreeCut", "emdbook", "forestplot", "ggplot2", "lpSolve", "matrixStats", "mclust", "pbapply", "plyr", "rlang", "scater", "smurf"] }, "alabaster": { "name": "alabaster", "version": "1.8.0", "sha256": "00av666zqam85k1zhv6a3b1k6233kd7mkqfr5ldr5zpp74rlarq6", "depends": ["alabaster_base", "alabaster_bumpy", "alabaster_mae", "alabaster_matrix", "alabaster_ranges", "alabaster_sce", "alabaster_se", "alabaster_spatial", "alabaster_string", "alabaster_vcf"] }, "alabaster_base": { "name": "alabaster.base", "version": "1.8.1", "sha256": "08ia5540l5qqsk7s0jwcwabgj1mi0lrnn34sm89n6cs9c8kyga6f", "depends": ["Rcpp", "Rhdf5lib", "S4Vectors", "alabaster_schemas", "assorthead", "jsonlite", "jsonvalidate", "rhdf5"] }, "alabaster_bumpy": { "name": "alabaster.bumpy", "version": "1.8.1", "sha256": "1axx1pz6ba7lb7n81rvykd7wyiz5ljbdnflmgr6vsr9l9m0sg3vj", "depends": ["BiocGenerics", "BumpyMatrix", "IRanges", "Matrix", "S4Vectors", "alabaster_base", "rhdf5"] }, "alabaster_files": { "name": "alabaster.files", "version": "1.6.0", "sha256": "1qcssc491v9zv6025vg0kma2dydi3pdjbmnjv3h6z9qcq5fpvb28", "depends": ["BiocGenerics", "Rsamtools", "S4Vectors", "alabaster_base"] }, "alabaster_mae": { "name": "alabaster.mae", "version": "1.8.0", "sha256": "0pfdfc6a1gpp5v4n3sjbhplk73sds22989wvmr1l7rf91v19xh10", "depends": ["MultiAssayExperiment", "S4Vectors", "alabaster_base", "alabaster_se", "jsonlite", "rhdf5"] }, "alabaster_matrix": { "name": "alabaster.matrix", "version": "1.8.0", "sha256": "176kmp9fgjdhsijh58zqsn9bmq28l1crgs7zqm9p4cga58549jaj", "depends": ["BiocGenerics", "DelayedArray", "HDF5Array", "Matrix", "Rcpp", "S4Arrays", "S4Vectors", "SparseArray", "alabaster_base", "rhdf5"] }, "alabaster_ranges": { "name": "alabaster.ranges", "version": "1.8.0", "sha256": "0xijg8rr7zq3jx0zp1pf9rkxlkgv0dg7n8dsn2aisy1lznz7l8cs", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "alabaster_base", "rhdf5"] }, "alabaster_sce": { "name": "alabaster.sce", "version": "1.8.0", "sha256": "06jhis9rinfa6b5d2aphcia4x52dwlh4rz4yrm7xy0ylix37p7vn", "depends": ["SingleCellExperiment", "alabaster_base", "alabaster_se", "jsonlite"] }, "alabaster_schemas": { "name": "alabaster.schemas", "version": "1.8.0", "sha256": "0gli9hs5c09b8mfga1r7xf50gxd2m6wyfkcqf0vxzk57zr9scq9w", "depends": [] }, "alabaster_se": { "name": "alabaster.se", "version": "1.8.0", "sha256": "1psl8dqw1x5zcyikf72libc4lzmjgczdfvmlc2xfrnd98ad5v9wi", "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "alabaster_base", "alabaster_matrix", "alabaster_ranges", "jsonlite"] }, "alabaster_sfe": { "name": "alabaster.sfe", "version": "1.0.0", "sha256": "068rs6hnh31vfby4kn43893d0g41853678fbwx740w2yj7k8c7l6", "depends": ["EBImage", "RBioFormats", "S4Vectors", "SingleCellExperiment", "SpatialFeatureExperiment", "SummarizedExperiment", "alabaster_base", "alabaster_sce", "alabaster_spatial", "jsonlite", "sfarrow", "spatialreg", "spdep", "terra", "xml2"] }, "alabaster_spatial": { "name": "alabaster.spatial", "version": "1.8.0", "sha256": "0q2x88bf28l008j1bgjna7g5xrig1wp180yqcqxifcjgi74hvjmy", "depends": ["S4Vectors", "SpatialExperiment", "alabaster_base", "alabaster_sce", "rhdf5"] }, "alabaster_string": { "name": "alabaster.string", "version": "1.8.0", "sha256": "0bb3am1ifqwgjj5qz0l991grsfhlxf1a49cy896f8n2hkhgra3sa", "depends": ["Biostrings", "S4Vectors", "alabaster_base"] }, "alabaster_vcf": { "name": "alabaster.vcf", "version": "1.8.0", "sha256": "12il80xwgynwalbh1ip3ly1p2nb6hs26zl03r4m2r8lp74ddzrpp", "depends": ["Rsamtools", "S4Vectors", "VariantAnnotation", "alabaster_base", "alabaster_se", "alabaster_string"] }, "alevinQC": { "name": "alevinQC", "version": "1.24.0", "sha256": "1ak04r3hhbbkqjmxdj81wra1pwjg58hq5i0gjkdh7f5vq64i5xsf", "depends": ["DT", "GGally", "Rcpp", "cowplot", "dplyr", "ggplot2", "rjson", "rlang", "rmarkdown", "shiny", "shinydashboard", "tximport"] }, "altcdfenvs": { "name": "altcdfenvs", "version": "2.70.0", "sha256": "0ga0v478q4ms8n3ad8nw1q5a48ghr04z3hk6vmmxirbkg7lzyjp6", "depends": ["Biobase", "BiocGenerics", "Biostrings", "S4Vectors", "affy", "hypergraph", "makecdfenv"] }, "amplican": { "name": "amplican", "version": "1.30.0", "sha256": "0y5bknkn6l32bk2ia0dv3c8pp2dx2n83iwhbqh0l13jajv8j1csd", "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "Matrix", "Rcpp", "S4Vectors", "ShortRead", "cluster", "data_table", "dplyr", "ggplot2", "ggthemes", "gridExtra", "gtable", "knitr", "matrixStats", "pwalign", "rmarkdown", "stringr", "waffle"] }, "animalcules": { "name": "animalcules", "version": "1.24.0", "sha256": "1i38rmggbblkv75kn5rc56zlkgm51slalqi3nvmh6y2ils68x1m6", "depends": ["DESeq2", "DT", "GUniFrac", "Matrix", "MultiAssayExperiment", "ROCit", "S4Vectors", "SummarizedExperiment", "XML", "ape", "assertthat", "caret", "covr", "dplyr", "forcats", "ggforce", "ggplot2", "lattice", "limma", "magrittr", "plotly", "rentrez", "reshape2", "scales", "shiny", "shinyjs", "tibble", "tidyr", "tsne", "umap", "vegan"] }, "annaffy": { "name": "annaffy", "version": "1.80.0", "sha256": "1ac95hxhvacvccw01x8g0yzqc3azx0h79pnxnv7cfihb0lpvd331", "depends": ["AnnotationDbi", "Biobase", "BiocManager", "DBI", "GO_db"] }, "annmap": { "name": "annmap", "version": "1.50.0", "sha256": "0xw75x0zgl7nzl4frxqcnj2fyzw59i1xzlwfnvs32c04bjnzmx30", "depends": ["Biobase", "BiocGenerics", "DBI", "GenomicRanges", "IRanges", "RMySQL", "Rsamtools", "digest", "genefilter", "lattice"] }, "annotate": { "name": "annotate", "version": "1.86.1", "sha256": "04xnr350xpb6wgrnafyis6yvzij69ybwvzcrld1anlfkky5iybkf", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "DBI", "XML", "httr", "xtable"] }, "annotationTools": { "name": "annotationTools", "version": "1.82.0", "sha256": "06p7lzib1br503clyib07lx17b9y8xmxz5yr6ajhbwd8qz2pj3k1", "depends": ["Biobase"] }, "annotatr": { "name": "annotatr", "version": "1.34.0", "sha256": "00d0q534apwnzal3xabgcgcd659zsg73xb3md756caipx7qlcam8", "depends": ["AnnotationDbi", "AnnotationHub", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "dplyr", "ggplot2", "readr", "regioneR", "reshape2", "rtracklayer"] }, "anota": { "name": "anota", "version": "1.56.0", "sha256": "1hbr8lyh8bjssyfq7p8g2ilpr2218ab8fravwr89s2nhiq557z5f", "depends": ["multtest", "qvalue"] }, "anota2seq": { "name": "anota2seq", "version": "1.30.0", "sha256": "0widc82rxb16ix61s66ppjxbin0mpda5l6a2194cxxfflxdziafb", "depends": ["DESeq2", "RColorBrewer", "SummarizedExperiment", "edgeR", "limma", "multtest", "qvalue"] }, "antiProfiles": { "name": "antiProfiles", "version": "1.48.0", "sha256": "1pf9fdafvaiy87s13455chgbym5najv58wfk5aw2yn7bmyvqcqnr", "depends": ["locfit", "matrixStats"] }, "apComplex": { "name": "apComplex", "version": "2.74.0", "sha256": "0a7k2a8i29a21d4ag3m33yvclsr13fm687hmnds7asy22fjid5lb", "depends": ["RBGL", "Rgraphviz", "graph", "org_Sc_sgd_db"] }, "apeglm": { "name": "apeglm", "version": "1.30.0", "sha256": "10va8admxwd71bql3biad66fzdl8ancdj37g7wzijbdhmss5y6k4", "depends": ["GenomicRanges", "Rcpp", "RcppEigen", "RcppNumerical", "SummarizedExperiment", "emdbook"] }, "appreci8R": { "name": "appreci8R", "version": "1.26.0", "sha256": "1ha8jalkjb8v98hn4kvg638wycl0gjyrpx76gcqz64d0c2197zka", "depends": ["BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "Biostrings", "COSMIC_67", "DT", "GenomicFeatures", "GenomicRanges", "GenomicScores", "Homo_sapiens", "IRanges", "MafDb_1Kgenomes_phase3_hs37d5", "MafDb_ExAC_r1_0_hs37d5", "MafDb_gnomADex_r2_1_hs37d5", "PolyPhen_Hsapiens_dbSNP131", "Rsamtools", "S4Vectors", "SIFT_Hsapiens_dbSNP137", "SNPlocs_Hsapiens_dbSNP144_GRCh37", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg19_knownGene", "VariantAnnotation", "XtraSNPlocs_Hsapiens_dbSNP144_GRCh37", "openxlsx", "rentrez", "seqinr", "shiny", "shinyjs", "stringr"] }, "aroma_light": { "name": "aroma.light", "version": "3.38.0", "sha256": "0i6b5mp7m61dy00scqmb2aa63fl9a9pxaf1zw13sdxj5xhpns7wa", "depends": ["R_methodsS3", "R_oo", "R_utils", "matrixStats"] }, "arrayMvout": { "name": "arrayMvout", "version": "1.66.0", "sha256": "1fp73lwfwdg9hyk4jja903bh6w5gnlhaqfk9wcjk22kcj35y6pn3", "depends": ["Biobase", "affy", "affyContam", "lumi", "mdqc", "parody"] }, "arrayQuality": { "name": "arrayQuality", "version": "1.86.0", "sha256": "09qv9hy0yjsdjmmigj5v1yng00km834pg95zhx4v371fvcf0iagk", "depends": ["RColorBrewer", "gridBase", "hexbin", "limma", "marray"] }, "arrayQualityMetrics": { "name": "arrayQualityMetrics", "version": "3.64.0", "sha256": "1kz2d40wx2ksy9dz1z3wylcj7y7ad9z8xphsnz39j02m4g5mbvlp", "depends": ["Biobase", "Hmisc", "RColorBrewer", "XML", "affy", "affyPLM", "beadarray", "genefilter", "gridSVG", "hwriter", "lattice", "latticeExtra", "limma", "setRNG", "svglite", "vsn"] }, "artMS": { "name": "artMS", "version": "1.26.0", "sha256": "18j9pq2llia7kxm5wkfd1w5qfjdfgx2c57hjn8kwfg10pnxpabmv", "depends": ["AnnotationDbi", "MSstats", "RColorBrewer", "UpSetR", "VennDiagram", "bit64", "circlize", "cluster", "corrplot", "data_table", "dplyr", "getopt", "ggdendro", "ggplot2", "ggrepel", "gplots", "limma", "openxlsx", "org_Hs_eg_db", "pheatmap", "plotly", "plyr", "scales", "seqinr", "stringr", "tidyr", "yaml"] }, "assorthead": { "name": "assorthead", "version": "1.2.0", "sha256": "15bj82llark5pr6w7ncf66vcaifplx2k1hiv0vdf2kmmjqblc03d", "depends": [] }, "atSNP": { "name": "atSNP", "version": "1.24.0", "sha256": "0c7w0pf91hhwa33xcbf5qx39lln29hdmz1w1lqd0011jgkazsgsr", "depends": ["BSgenome", "BiocFileCache", "BiocParallel", "Rcpp", "data_table", "ggplot2", "lifecycle", "motifStack", "rappdirs", "testthat"] }, "atena": { "name": "atena", "version": "1.14.1", "sha256": "149b2hx8bvgmy9qdg5cm5icx8xi2pj0ysfaxisvrh1500rwh6kf8", "depends": ["AnnotationHub", "BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "MatrixGenerics", "Rsamtools", "S4Vectors", "SQUAREM", "SummarizedExperiment", "cli", "matrixStats", "sparseMatrixStats"] }, "attract": { "name": "attract", "version": "1.60.0", "sha256": "1a0kcmp97j565g2f2xwf5nm3bqvp4w3rksgj97s2cn64g2gyn1jw", "depends": ["AnnotationDbi", "Biobase", "GOstats", "KEGGREST", "cluster", "limma", "org_Hs_eg_db", "reactome_db"] }, "autonomics": { "name": "autonomics", "version": "1.16.0", "sha256": "1n3v27k5jzaj94sf6nqvzkifidw283j1n6skw9hhl8cvmwqhdda2", "depends": ["BiocFileCache", "BiocGenerics", "MultiAssayExperiment", "RColorBrewer", "R_utils", "S4Vectors", "SummarizedExperiment", "abind", "bit64", "cluster", "codingMatrices", "colorspace", "data_table", "dplyr", "edgeR", "ggforce", "ggplot2", "ggrepel", "gridExtra", "limma", "magrittr", "matrixStats", "readxl", "rlang", "scales", "stringi", "survival", "tidyr", "tidyselect", "vsn"] }, "awst": { "name": "awst", "version": "1.16.0", "sha256": "0fphbg5q1dh3khw7vjkkajmmn6rd9wq0l9r6gdk759lnn0nvx26j", "depends": ["SummarizedExperiment"] }, "bacon": { "name": "bacon", "version": "1.36.0", "sha256": "1af7186valdc32rgn2ab0vjsqmdwjvyryv1pqwpfsrr0q6lcrkih", "depends": ["BiocParallel", "ellipse", "ggplot2"] }, "ballgown": { "name": "ballgown", "version": "2.40.0", "sha256": "0zcim1yahbmyajyz4b8iw7zb52m1b0gfg6mflqv9440dqp1fwnvi", "depends": ["Biobase", "GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "limma", "rtracklayer", "sva"] }, "bambu": { "name": "bambu", "version": "3.10.1", "sha256": "0asx4b1kw7zp9yyw3lk1ibb1c559y9s69klrsqx4d0radkcb61p4", "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rcpp", "RcppArmadillo", "Rsamtools", "S4Vectors", "SummarizedExperiment", "data_table", "dplyr", "tidyr", "xgboost"] }, "bamsignals": { "name": "bamsignals", "version": "1.40.0", "sha256": "0bjmsciw3rrn8pid5yq5pn18w52gks6p41syggv5w21pfj3vdqxa", "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "Rcpp", "Rhtslib", "zlibbioc"] }, "bandle": { "name": "bandle", "version": "1.12.0", "sha256": "1ss70psnr5avk6ny6hgasx3c2yxr6slrw2xk6wga64l0aiyki4d1", "depends": ["BH", "Biobase", "BiocParallel", "BiocStyle", "MSnbase", "RColorBrewer", "Rcpp", "RcppArmadillo", "S4Vectors", "circlize", "coda", "dplyr", "ggalluvial", "ggplot2", "ggrepel", "gridExtra", "gtools", "knitr", "lbfgs", "pRoloc", "pRolocdata", "plyr", "rlang", "robustbase", "tidyr"] }, "banocc": { "name": "banocc", "version": "1.32.0", "sha256": "1y2zmym9l5d2ny6vjzwc192cbgkszmglmb23xmcqrzr1q34i2vc7", "depends": ["coda", "mvtnorm", "rstan", "stringr"] }, "barbieQ": { "name": "barbieQ", "version": "1.0.1", "sha256": "1vl6c6mrkdkjg3ll4j2n1fg31wgdlh55cgm3by39kxp4rf76m5mq", "depends": ["ComplexHeatmap", "S4Vectors", "SummarizedExperiment", "circlize", "data_table", "dplyr", "ggplot2", "igraph", "limma", "logistf", "magrittr", "tidyr"] }, "barcodetrackR": { "name": "barcodetrackR", "version": "1.16.0", "sha256": "1n2rj50gwqmqj5gs5d3asd3gcs0iv1rr1zh12s55lcsdxyfgp1ar", "depends": ["RColorBrewer", "S4Vectors", "SummarizedExperiment", "circlize", "cowplot", "dplyr", "ggdendro", "ggplot2", "ggridges", "magrittr", "plyr", "proxy", "rlang", "scales", "shiny", "tibble", "tidyr", "vegan", "viridis"] }, "basecallQC": { "name": "basecallQC", "version": "1.32.0", "sha256": "00p17azjppzfji35ps3j9cspyi4x5ikwnympkhmdkf1l816ijwb6", "depends": ["DT", "ShortRead", "XML", "data_table", "dplyr", "ggplot2", "knitr", "lazyeval", "magrittr", "prettydoc", "raster", "rmarkdown", "stringr", "tidyr", "yaml"] }, "basilisk": { "name": "basilisk", "version": "1.20.0", "sha256": "05j16g9bamd7k2h4j2mnmdlmvivwzsjmjjld0k67jvlza7lynayb", "depends": ["basilisk_utils", "dir_expiry", "reticulate"] }, "basilisk_utils": { "name": "basilisk.utils", "version": "1.20.0", "sha256": "12wfmyq2as6vfg94fnlw4hxi6y8gw45x27hbh99mkn496vqng575", "depends": ["dir_expiry"] }, "batchelor": { "name": "batchelor", "version": "1.24.0", "sha256": "1bffk38xa8p0zhhz4bav3i3jc2ih85zrzl1in2yfplqnk8wlfq2z", "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "DelayedArray", "DelayedMatrixStats", "Matrix", "Rcpp", "ResidualMatrix", "S4Vectors", "ScaledMatrix", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "beachmat", "igraph", "scuttle"] }, "bayNorm": { "name": "bayNorm", "version": "1.26.0", "sha256": "0k3a66p4hsbv3k6brd8vj5n87hr82s2mzys3n9zc1qzdykjylh4f", "depends": ["BB", "BiocParallel", "MASS", "Matrix", "Rcpp", "RcppArmadillo", "RcppProgress", "SingleCellExperiment", "SummarizedExperiment", "doSNOW", "fitdistrplus", "foreach", "iterators", "locfit"] }, "baySeq": { "name": "baySeq", "version": "2.42.0", "sha256": "030r5xlimmn6mwmkyrm8jwb0jg5nfbzmdv17gss4c9pmpkahs18v", "depends": ["GenomicRanges", "abind", "edgeR"] }, "bcSeq": { "name": "bcSeq", "version": "1.30.0", "sha256": "084sqic3wzklh34s2h33ml7ylb5si7ss50pwnjq9zqw4jqd8pb9r", "depends": ["Biostrings", "Matrix", "Rcpp"] }, "beachmat": { "name": "beachmat", "version": "2.24.0", "sha256": "0hf1x1lmzchl2imyw0cbf17akcyjpwifz627v85nkj1lngygd865", "depends": ["BiocGenerics", "DelayedArray", "Matrix", "Rcpp", "SparseArray", "assorthead"] }, "beachmat_hdf5": { "name": "beachmat.hdf5", "version": "1.6.0", "sha256": "061x88pqi2nksxm8kfcn817ggk6i9256krf63cvfzj8why3w7sjj", "depends": ["DelayedArray", "HDF5Array", "Rcpp", "Rhdf5lib", "assorthead", "beachmat"] }, "beachmat_tiledb": { "name": "beachmat.tiledb", "version": "1.0.0", "sha256": "1dsaxvf1vlimi08jdx41m07ypcbn56jprv4s1dyv3kypi0kx103f", "depends": ["DelayedArray", "Rcpp", "TileDBArray", "assorthead", "beachmat", "tiledb"] }, "beadarray": { "name": "beadarray", "version": "2.58.0", "sha256": "0m9hmy4xn7q2v4ra95b9h08d0qh5qmjgqmg96vabyv46gn5i7qp4", "depends": ["AnnotationDbi", "BeadDataPackR", "Biobase", "BiocGenerics", "GenomicRanges", "IRanges", "ggplot2", "hexbin", "illuminaio", "limma", "reshape2"] }, "bedbaser": { "name": "bedbaser", "version": "1.0.3", "sha256": "1h52xsw5bvzjj633wz9jxd4z3b75bw8w86p9vnb7dc9kcrzanp3l", "depends": ["AnVIL", "BiocFileCache", "GenomeInfoDb", "GenomicRanges", "R_utils", "dplyr", "httr", "purrr", "rlang", "rtracklayer", "stringr", "tibble", "tidyr"] }, "beer": { "name": "beer", "version": "1.12.0", "sha256": "1g88qs5hkgj48fqi067p3p1pav220368i06fpjizpbnl8c4p8a77", "depends": ["BiocParallel", "PhIPData", "SummarizedExperiment", "cli", "edgeR", "progressr", "rjags"] }, "benchdamic": { "name": "benchdamic", "version": "1.14.3", "sha256": "0xc05qghdr2xynf5gk695xbpb5hj0wrfcjps34h8cqd249by2dk6", "depends": ["ALDEx2", "ANCOMBC", "BiocParallel", "DESeq2", "GUniFrac", "MAST", "MGLM", "Maaslin2", "MicrobiomeStat", "NOISeq", "RColorBrewer", "Seurat", "SummarizedExperiment", "TreeSummarizedExperiment", "corncob", "cowplot", "dearseq", "edgeR", "ggdendro", "ggplot2", "ggridges", "limma", "lme4", "maaslin3", "metagenomeSeq", "microbiome", "mixOmics", "phyloseq", "plyr", "reshape2", "tidytext", "zinbwave"] }, "betaHMM": { "name": "betaHMM", "version": "1.4.1", "sha256": "0rkjnqbmxxkb4f3n4z8g2h4pbgp379vwdyvgsk6cqqzl4lnkzfns", "depends": ["GenomicRanges", "S4Vectors", "SummarizedExperiment", "cowplot", "doParallel", "dplyr", "foreach", "ggplot2", "pROC", "scales", "stringr", "tidyr", "tidyselect"] }, "bettr": { "name": "bettr", "version": "1.4.0", "sha256": "0qbxxrjddb0h4m2xx2f40c85vzhxhq2nmfyga6l8ms6f7ljfpybh", "depends": ["ComplexHeatmap", "DT", "Hmisc", "S4Vectors", "SummarizedExperiment", "bslib", "circlize", "cowplot", "dplyr", "ggplot2", "rlang", "scales", "shiny", "shinyjqui", "sortable", "tibble", "tidyr"] }, "bigmelon": { "name": "bigmelon", "version": "1.34.0", "sha256": "1g0jp0l5fb91ys07ks64q8vi759phpfifrlvjz463xy7qd42z8kj", "depends": ["Biobase", "BiocGenerics", "GEOquery", "gdsfmt", "illuminaio", "methylumi", "minfi", "wateRmelon"] }, "bioCancer": { "name": "bioCancer", "version": "1.36.0", "sha256": "18rgnbqipbkb6gjscnsb88zqwi1qm7q4fhsy6py76mxyzar4kcrw", "depends": ["AlgDesign", "AnnotationDbi", "Biobase", "DOSE", "DT", "DiagrammeR", "GO_db", "R_methodsS3", "R_oo", "ReactomePA", "XML", "cBioPortalData", "clusterProfiler", "dplyr", "geNetClassifier", "htmlwidgets", "org_Bt_eg_db", "org_Hs_eg_db", "plyr", "r_import", "radiant_data", "reactome_db", "shiny", "shinythemes", "tibble", "tidyr", "visNetwork"] }, "bioDist": { "name": "bioDist", "version": "1.80.0", "sha256": "0nkbg6bv72bzfkqqr8y9rfl6wi74w188wmvpdcc4mjj59w6pv18n", "depends": ["Biobase", "KernSmooth"] }, "bioassayR": { "name": "bioassayR", "version": "1.46.0", "sha256": "17wv3yx9pgkpp1zvrk7w3df9x3rp3bf52ixvwsrpb7sh0j47cwbr", "depends": ["BiocGenerics", "ChemmineR", "DBI", "Matrix", "RSQLite", "XML", "rjson"] }, "biobroom": { "name": "biobroom", "version": "1.40.0", "sha256": "13c5cj8wmkhrghri5vrwrb3vzxs7vmcxn5ffib1rckxdm65hxby7", "depends": ["Biobase", "broom", "dplyr", "tidyr"] }, "biobtreeR": { "name": "biobtreeR", "version": "1.20.0", "sha256": "0fdim4k0s5f70xbbf4cbr7idha8w4sfv327l94cfmzh5k3zxdm1a", "depends": ["httpuv", "httr", "jsonlite", "stringi"] }, "biocGraph": { "name": "biocGraph", "version": "1.70.0", "sha256": "0iy7xg4yrsb1n0ggpzin9ll9hf80yxplvdiymahhpv6kp7c8l0mk", "depends": ["BiocGenerics", "Rgraphviz", "geneplotter", "graph"] }, "biocViews": { "name": "biocViews", "version": "1.76.0", "sha256": "1572jbg29lvnn1gan47mfqj7fn33hv9fw1bdvprjfmabq9n2cv9r", "depends": ["Biobase", "BiocManager", "RBGL", "RCurl", "RUnit", "XML", "graph"] }, "biocmake": { "name": "biocmake", "version": "1.0.1", "sha256": "0ajcq62xcqc9kj8h236lkw67z72b5vkymhpn1vlspmhx005frcq3", "depends": ["dir_expiry"] }, "biocroxytest": { "name": "biocroxytest", "version": "1.4.0", "sha256": "1m35dw7j0jld0fpgn3vbhdh0rrz7f8lljasf79y54mga4shragls", "depends": ["cli", "glue", "roxygen2", "stringr"] }, "biocthis": { "name": "biocthis", "version": "1.18.0", "sha256": "06kjalns95273p3bfbnj1349zmyvmmmkdqhbingjfczgaz8sfnv5", "depends": ["BiocManager", "fs", "glue", "rlang", "styler", "usethis"] }, "biodb": { "name": "biodb", "version": "1.16.0", "sha256": "1xja9fl4yskqj2b51smddnpqgzi5i3w4ap18rwlpw9ci07rafyk5", "depends": ["BiocFileCache", "R6", "RCurl", "RSQLite", "Rcpp", "XML", "chk", "git2r", "jsonlite", "lgr", "lifecycle", "openssl", "plyr", "progress", "rappdirs", "stringr", "testthat", "withr", "yaml"] }, "biodbChebi": { "name": "biodbChebi", "version": "1.14.0", "sha256": "0z2xrc6qpipiw6s00nlh4wp8k2xwx8h18g40bk7kdji3l9fvx73p", "depends": ["R6", "biodb"] }, "biodbHmdb": { "name": "biodbHmdb", "version": "1.14.0", "sha256": "0xpc2dygjm8gy7612ggk2kgd599859l0i8qdjzx01vvchckkps5h", "depends": ["R6", "Rcpp", "biodb", "testthat", "zip"] }, "biodbNcbi": { "name": "biodbNcbi", "version": "1.12.0", "sha256": "19f37fgbhb22k27riklbdary3a1ybnm7drapfkss7grizwpa9d0x", "depends": ["R6", "XML", "biodb", "chk"] }, "biodbNci": { "name": "biodbNci", "version": "1.12.0", "sha256": "10fyx0mdhllqlykhm3xnv59hw0ham27wgnswapk0a36rr804mfpj", "depends": ["R6", "Rcpp", "biodb", "chk", "testthat"] }, "biodbUniprot": { "name": "biodbUniprot", "version": "1.14.0", "sha256": "1m27a7ngn4gwhj37vwg2mq5588q3cp85fcq5fjbjygi7l3d3pwg3", "depends": ["R6", "biodb"] }, "biomaRt": { "name": "biomaRt", "version": "2.64.0", "sha256": "1yyzl573jyv61q6q3h36k7as6nkgh7cpxz5i4f28q6yfcz2imjsz", "depends": ["AnnotationDbi", "BiocFileCache", "curl", "digest", "httr2", "progress", "rappdirs", "stringr", "xml2"] }, "biomformat": { "name": "biomformat", "version": "1.36.0", "sha256": "0dlwfm0hkyh2y21grbjbrq26ix5f8jq1rbnqwklq6v85kf6ddhb6", "depends": ["Matrix", "jsonlite", "plyr", "rhdf5"] }, "biomvRCNS": { "name": "biomvRCNS", "version": "1.48.0", "sha256": "0wbca3hyc0k1r6l7c4rl0m4447jy9svjmxz7fm6jk29afchxa1jh", "depends": ["GenomicRanges", "Gviz", "IRanges", "mvtnorm"] }, "biosigner": { "name": "biosigner", "version": "1.36.4", "sha256": "1yrr8lsg05m8y57snsk3jpzj29kfl2264gr3d49lsmsnpnrg9h6h", "depends": ["Biobase", "MultiAssayExperiment", "MultiDataSet", "SummarizedExperiment", "e1071", "randomForest", "ropls"] }, "biotmle": { "name": "biotmle", "version": "1.32.1", "sha256": "0wic1c2h0bf6r2yv98xcl665lg549gvc1l6av8b2ad6cs13a5fms", "depends": ["BiocGenerics", "BiocParallel", "S4Vectors", "SummarizedExperiment", "assertthat", "dplyr", "drtmle", "ggplot2", "ggsci", "limma", "superheat", "tibble"] }, "biovizBase": { "name": "biovizBase", "version": "1.56.0", "sha256": "14xlvcjf1w283rb3249hzh9k8c2w2z8fimh0qsjnzhm1l82dihga", "depends": ["AnnotationDbi", "AnnotationFilter", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Hmisc", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "dichromat", "ensembldb", "rlang", "scales"] }, "biscuiteer": { "name": "biscuiteer", "version": "1.22.0", "sha256": "03q31l3cljvb6vqbdxdhpjfy39fw0gk043l5dkzwpwxirimw4kgn", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "DelayedMatrixStats", "GenomeInfoDb", "GenomicRanges", "HDF5Array", "Homo_sapiens", "IRanges", "Matrix", "Mus_musculus", "QDNAseq", "R_utils", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "biscuiteerData", "bsseq", "data_table", "dmrseq", "gtools", "impute", "matrixStats", "qualV", "readr", "rtracklayer"] }, "blacksheepr": { "name": "blacksheepr", "version": "1.22.0", "sha256": "05ywzx7sbx1bas24hl36d52a3bzclm22q7nwpvfraxv2d9k8dvpd", "depends": ["ComplexHeatmap", "RColorBrewer", "SummarizedExperiment", "circlize", "pasilla", "viridis"] }, "blima": { "name": "blima", "version": "1.42.0", "sha256": "0hsgd1zl3i2v4916c7dxlwlpm3affmgpb9s58p9rj1as3nvk6z9l", "depends": ["Biobase", "BiocGenerics", "Rcpp", "beadarray"] }, "bluster": { "name": "bluster", "version": "1.18.0", "sha256": "0q51rpjj2m61ax2n192pcbaix26f3jxjl5pk09w5mcppr6cym0hi", "depends": ["BiocNeighbors", "BiocParallel", "Matrix", "Rcpp", "S4Vectors", "assorthead", "cluster", "igraph"] }, "bnbc": { "name": "bnbc", "version": "1.30.0", "sha256": "0ly0hb5893fblxjz5jmbsyd4452dxwcd0wzkfzw7p4f4qmfrqqlm", "depends": ["BiocGenerics", "EBImage", "GenomeInfoDb", "GenomicRanges", "HiCBricks", "IRanges", "Rcpp", "S4Vectors", "SummarizedExperiment", "data_table", "matrixStats", "preprocessCore", "rhdf5", "sva"] }, "bnem": { "name": "bnem", "version": "1.16.0", "sha256": "00ynmwi9zf2sbprr2lcahrjfvcz34cnrpp7n0haa3f5dsccr9cfw", "depends": ["Biobase", "CellNOptR", "RColorBrewer", "Rgraphviz", "affy", "binom", "cluster", "epiNEM", "flexclust", "graph", "limma", "matrixStats", "mnem", "rmarkdown", "snowfall", "sva", "vsn"] }, "borealis": { "name": "borealis", "version": "1.12.0", "sha256": "1k5qjg1nndmdbpynjivlh5xy44y1b0q29g9f7rmxx9c8r2pg6pmj", "depends": ["Biobase", "DSS", "GenomicRanges", "R_utils", "bsseq", "cowplot", "doParallel", "dplyr", "foreach", "gamlss", "gamlss_dist", "ggplot2", "plyr", "purrr", "rlang", "snow"] }, "branchpointer": { "name": "branchpointer", "version": "1.34.0", "sha256": "0n3linwha0lj65m72k7zm2bslxkdkjb1yqgs5ksdxrlziwmfs2nj", "depends": ["BSgenome_Hsapiens_UCSC_hg38", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "biomaRt", "caret", "cowplot", "data_table", "gbm", "ggplot2", "kernlab", "plyr", "rtracklayer", "stringr"] }, "breakpointR": { "name": "breakpointR", "version": "1.26.0", "sha256": "12sns2h0m5w9jp4yr9f0i9v77v2a7r64cakqkmrjm4svciqaj6n5", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "breakpointRdata", "cowplot", "doParallel", "foreach", "ggplot2", "gtools"] }, "brendaDb": { "name": "brendaDb", "version": "1.22.0", "sha256": "1libb78j7i03fw6y5bpv45aljmllysv7yn80yx3whvzzxzn4h1ss", "depends": ["BiocFileCache", "BiocParallel", "Rcpp", "crayon", "dplyr", "magrittr", "purrr", "rappdirs", "rlang", "stringr", "tibble", "tidyr"] }, "broadSeq": { "name": "broadSeq", "version": "1.2.4", "sha256": "00xqpr915yhimmimbr43010ljdj7fiq613a3yq6haxvkqjpv83ri", "depends": ["BiocStyle", "DELocal", "DESeq2", "EBSeq", "NOISeq", "SummarizedExperiment", "clusterProfiler", "dplyr", "edgeR", "forcats", "genefilter", "ggplot2", "ggplotify", "ggpubr", "pheatmap", "plyr", "purrr", "sechm", "stringr"] }, "bsseq": { "name": "bsseq", "version": "1.44.1", "sha256": "1bxrsjva4vxs65wiv6rchwinikyk3v2d2rnnzpm9cmslshxs1y9r", "depends": ["BSgenome", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "DelayedArray", "DelayedMatrixStats", "GenomeInfoDb", "GenomicRanges", "HDF5Array", "IRanges", "R_utils", "Rcpp", "S4Vectors", "SummarizedExperiment", "assorthead", "beachmat", "data_table", "gtools", "limma", "locfit", "permute", "rhdf5", "scales"] }, "bugsigdbr": { "name": "bugsigdbr", "version": "1.14.3", "sha256": "0ymr4di7daf5n0jy71lbn5wlyvdpid64n80inlvgf3n6w1qf76h4", "depends": ["BiocFileCache", "vroom"] }, "bumphunter": { "name": "bumphunter", "version": "1.50.0", "sha256": "05dsx5a3xagq6jajkcg6dzd43w5b4nbjqhjkl1wvg5va3dx4hl5z", "depends": ["AnnotationDbi", "BiocGenerics", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "doRNG", "foreach", "iterators", "limma", "locfit", "matrixStats"] }, "cBioPortalData": { "name": "cBioPortalData", "version": "2.20.0", "sha256": "1if4dkzlx9zclk0n32a4bc8sy3dxf9nrzgacy095lbp83qs1najc", "depends": ["AnVIL", "BiocBaseUtils", "BiocFileCache", "GenomeInfoDb", "GenomicRanges", "IRanges", "MultiAssayExperiment", "RTCGAToolbox", "RaggedExperiment", "S4Vectors", "SummarizedExperiment", "TCGAutils", "digest", "dplyr", "httr", "readr", "tibble", "tidyr"] }, "cTRAP": { "name": "cTRAP", "version": "1.26.0", "sha256": "0l14km7mn8lf19wg4vydid0r2q84mw7wakfx6kwzgjzb6kgar4xb", "depends": ["AnnotationDbi", "AnnotationHub", "DT", "R_utils", "binr", "cowplot", "data_table", "dplyr", "fastmatch", "fgsea", "ggplot2", "ggrepel", "highcharter", "htmltools", "httr", "limma", "pbapply", "purrr", "qs", "readxl", "reshape2", "rhdf5", "rlang", "scales", "shiny", "shinycssloaders", "tibble"] }, "cageminer": { "name": "cageminer", "version": "1.14.0", "sha256": "0qmvzjk08p547qjmjrmgk4n647qmy9v3djdic8hygkkq1ii9ilbp", "depends": ["BioNERO", "GenomeInfoDb", "GenomicRanges", "IRanges", "ggbio", "ggplot2", "ggtext", "reshape2", "rlang"] }, "calm": { "name": "calm", "version": "1.22.0", "sha256": "01m2rpdmn0479x91i6g02m4fxrg5s5yj5vvmivklf32gb366s4s0", "depends": ["mgcv"] }, "canceR": { "name": "canceR", "version": "1.42.0", "sha256": "15a4pic5hbxhs89bhv074jl43222idin3zqxxph8nmmcpg8an215", "depends": ["Biobase", "Formula", "GSEABase", "RUnit", "R_methodsS3", "R_oo", "cBioPortalData", "circlize", "dplyr", "geNetClassifier", "phenoTest", "plyr", "rpart", "survival", "tidyr", "tkrplot"] }, "cancerclass": { "name": "cancerclass", "version": "1.52.0", "sha256": "106wizfqbxjnxyzi5jyhpg6yck6kcxw6k7xb2qx2w1bk5pgiks95", "depends": ["Biobase", "binom"] }, "cardelino": { "name": "cardelino", "version": "1.10.0", "sha256": "1apnzwia944cclsdc3x8plp87id3sd0qyz6xg2m61cl18nq17wl7", "depends": ["GenomeInfoDb", "GenomicRanges", "Matrix", "S4Vectors", "VariantAnnotation", "combinat", "ggplot2", "ggtree", "matrixStats", "pheatmap", "snpStats", "vcfR"] }, "casper": { "name": "casper", "version": "2.42.0", "sha256": "02ncaglam553874ygp9ddr37xkpvhpqpvkncy4czwsblqhnzpla1", "depends": ["Biobase", "BiocGenerics", "EBarrays", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "VGAM", "coda", "gaga", "gtools", "limma", "mgcv", "rtracklayer", "sqldf", "survival"] }, "categoryCompare": { "name": "categoryCompare", "version": "1.52.0", "sha256": "13qm189x70l6nnspwdy612i5f0l31ljrgiz78fjrh5nplmgffr4l", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "Category", "GOstats", "GSEABase", "RCy3", "annotate", "colorspace", "graph", "hwriter"] }, "cbaf": { "name": "cbaf", "version": "1.30.0", "sha256": "1qdlv8pls8fif1qlc30xmzd8vf3l09srpabzy397pj28x3j9xp88", "depends": ["BiocFileCache", "RColorBrewer", "cBioPortalData", "genefilter", "gplots", "openxlsx", "zip"] }, "cbpManager": { "name": "cbpManager", "version": "1.16.0", "sha256": "06hk0mrc9pz2wic5gil0zacnhwqq0ar1j9b63cr4xxgy7r2wmk6k", "depends": ["DT", "basilisk", "dplyr", "htmltools", "jsonlite", "magrittr", "markdown", "plyr", "rapportools", "reticulate", "rintrojs", "rlang", "shiny", "shinyBS", "shinycssloaders", "shinydashboard", "vroom"] }, "ccImpute": { "name": "ccImpute", "version": "1.10.0", "sha256": "0p2qglfy5wlsqs45z223wd4ym4kzhl9l9ww0ay7vrynsnzh1216n", "depends": ["BiocParallel", "Matrix", "Rcpp", "RcppEigen", "SingleCellExperiment", "SummarizedExperiment", "irlba", "sparseMatrixStats"] }, "ccfindR": { "name": "ccfindR", "version": "1.28.0", "sha256": "1203v7shhcrazq2jz9s79dvdqnz07a5hpa50g1w8wl539pzf2x8p", "depends": ["Matrix", "RColorBrewer", "Rcpp", "RcppEigen", "Rdpack", "Rmpi", "Rtsne", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "ape", "gtools", "irlba"] }, "ccmap": { "name": "ccmap", "version": "1.34.0", "sha256": "1khc7n1qpm7f4mpqy4qa74v03q581knig30hbvcd0a5x8gk8bvj3", "depends": ["AnnotationDbi", "BiocManager", "ccdata", "data_table", "doParallel", "foreach", "lsa", "xgboost"] }, "ccrepe": { "name": "ccrepe", "version": "1.44.0", "sha256": "07lxcz5mmj33dam2mvzr7a3crinjydvlxzsavncnnlgy8m7156lh", "depends": ["infotheo"] }, "ceRNAnetsim": { "name": "ceRNAnetsim", "version": "1.20.0", "sha256": "0whd1gd7r66pcxzy5mjxg9nfdm9gw56lrr9afzxdrknys2dc8kk6", "depends": ["dplyr", "furrr", "future", "ggplot2", "ggraph", "igraph", "purrr", "rlang", "tibble", "tidygraph", "tidyr"] }, "celaref": { "name": "celaref", "version": "1.26.0", "sha256": "1c0lgrx4p5prdv6byl0gm7qm928lw9z1d5g3005l21hf5qv4zxs2", "depends": ["BiocGenerics", "DelayedArray", "MAST", "Matrix", "S4Vectors", "SummarizedExperiment", "dplyr", "ggplot2", "magrittr", "readr", "rlang", "tibble"] }, "celda": { "name": "celda", "version": "1.24.0", "sha256": "08v99r9g0jcjnwh6vlpvlnzpxgnjqry5jh384m4v4m253jwz544l", "depends": ["ComplexHeatmap", "DelayedArray", "MCMCprecision", "Matrix", "RColorBrewer", "Rcpp", "RcppEigen", "Rtsne", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "circlize", "data_table", "dbscan", "dendextend", "digest", "doParallel", "enrichR", "foreach", "ggdendro", "ggplot2", "ggrepel", "gridExtra", "gtable", "matrixStats", "pROC", "plyr", "reshape2", "scales", "scater", "scran", "stringr", "uwot", "withr"] }, "cellbaseR": { "name": "cellbaseR", "version": "1.32.0", "sha256": "1ih99x5bjqvmbh49n3shkx789fcvpysmnrxzmfpz9mzz8wdi0gn7", "depends": ["BiocParallel", "R_utils", "Rsamtools", "data_table", "doParallel", "foreach", "httr", "jsonlite", "pbapply", "tidyr"] }, "cellity": { "name": "cellity", "version": "1.36.0", "sha256": "1d23gkfba6ym7qhkm9mydsslnizh549xjlv86nkaf4pnvpcbjc8s", "depends": ["AnnotationDbi", "e1071", "ggplot2", "mvoutlier", "org_Hs_eg_db", "org_Mm_eg_db", "robustbase", "topGO"] }, "cellmigRation": { "name": "cellmigRation", "version": "1.16.0", "sha256": "18bq8hml1pa7w5dw2lil7dlb5wrma99l46djklrg479872m8f5vd", "depends": ["FME", "FactoMineR", "Hmisc", "SpatialTools", "doParallel", "foreach", "matrixStats", "reshape2", "sp", "tiff", "vioplot"] }, "cellscape": { "name": "cellscape", "version": "1.32.0", "sha256": "009f2yfqnrcm61hm1nvl9hvxmpxk257ycw9a3lymvi255wxq4xr0", "depends": ["dplyr", "gtools", "htmlwidgets", "jsonlite", "reshape2", "stringr"] }, "cellxgenedp": { "name": "cellxgenedp", "version": "1.12.1", "sha256": "0gc7vp94vrrqqdxmcdbvvarx3g3196jyzcpwaap8f5glkfvwc8yz", "depends": ["DT", "cli", "curl", "dplyr", "httr", "rjsoncons", "shiny"] }, "censcyt": { "name": "censcyt", "version": "1.16.0", "sha256": "0hxbjx6as76n5nh03nfznl7x128pgr8p6xvyw5w1w6834zdzarha", "depends": ["BiocParallel", "MASS", "S4Vectors", "SummarizedExperiment", "broom_mixed", "diffcyt", "dirmult", "dplyr", "edgeR", "fitdistrplus", "lme4", "magrittr", "mice", "multcomp", "purrr", "rlang", "stringr", "survival", "tibble", "tidyr"] }, "cfDNAPro": { "name": "cfDNAPro", "version": "1.14.0", "sha256": "078878mfqsvnl2bxa3qlw80ld3lql0h2amzg5x5jsga0j8lhwldy", "depends": ["BSgenome_Hsapiens_NCBI_GRCh38", "BSgenome_Hsapiens_UCSC_hg19", "BSgenome_Hsapiens_UCSC_hg38", "BiocGenerics", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "dplyr", "ggplot2", "magrittr", "plyranges", "quantmod", "rlang", "stringr", "tibble"] }, "cfTools": { "name": "cfTools", "version": "1.8.0", "sha256": "02mqfjvlhczbv2l55sif2b95x78vp59r8lml9vdzv0jyjrbi8q15", "depends": ["BH", "GenomicRanges", "R_utils", "Rcpp", "basilisk", "cfToolsData"] }, "cfdnakit": { "name": "cfdnakit", "version": "1.6.0", "sha256": "0bcb1cp6f3w8sy038hhl3s6m2h91z2s74giv806gpzsb2wzpxgfa", "depends": ["Biobase", "GenomeInfoDb", "GenomicRanges", "IRanges", "PSCBS", "QDNAseq", "Rsamtools", "S4Vectors", "dplyr", "ggplot2", "magrittr", "rlang"] }, "cghMCR": { "name": "cghMCR", "version": "1.66.0", "sha256": "1ygk4j9j296ybnqxdr5p41akvhn2na1rm3icnpcf6zmm36xlvpww", "depends": ["BiocGenerics", "CNTools", "DNAcopy", "limma"] }, "chevreulPlot": { "name": "chevreulPlot", "version": "1.0.0", "sha256": "0lb34gxyaqxcjnhkyc63b9gfiw28hqg4l6myynmxa4xs5054paip", "depends": ["ComplexHeatmap", "EnsDb_Hsapiens_v86", "S4Vectors", "SingleCellExperiment", "chevreulProcess", "circlize", "cluster", "clustree", "dplyr", "forcats", "fs", "ggplot2", "patchwork", "plotly", "purrr", "scales", "scater", "scran", "scuttle", "stringr", "tibble", "tidyr", "tidyselect", "wiggleplotr"] }, "chevreulProcess": { "name": "chevreulProcess", "version": "1.0.0", "sha256": "01a2hihlbyvanf34z2ajnkfg3glib6bq6rnay7dl3q1dbygk9w8f", "depends": ["DBI", "EnsDb_Hsapiens_v86", "GenomicFeatures", "RSQLite", "S4Vectors", "SingleCellExperiment", "batchelor", "bluster", "circlize", "cluster", "dplyr", "ensembldb", "fs", "glue", "megadepth", "purrr", "scater", "scran", "scuttle", "stringr", "tibble", "tidyr", "tidyselect"] }, "chevreulShiny": { "name": "chevreulShiny", "version": "1.0.0", "sha256": "0cl1wx66wk2l206yjvhnjmdacn3vbci6gzxii5djqiisr8zp42ml", "depends": ["ComplexHeatmap", "DBI", "DT", "DataEditR", "EnhancedVolcano", "RSQLite", "S4Vectors", "SingleCellExperiment", "alabaster_base", "chevreulPlot", "chevreulProcess", "clustree", "dplyr", "fs", "future", "ggplot2", "ggplotify", "patchwork", "plotly", "purrr", "rappdirs", "readr", "scales", "shiny", "shinyFiles", "shinyWidgets", "shinydashboard", "shinyhelper", "shinyjs", "stringr", "tibble", "tidyr", "tidyselect", "waiter", "wiggleplotr"] }, "chihaya": { "name": "chihaya", "version": "1.8.0", "sha256": "164rhh0qf0c2vfr71admiwhrkr79kg3hby22cx5sifwaml3wmw7m", "depends": ["DelayedArray", "HDF5Array", "Matrix", "Rcpp", "Rhdf5lib", "rhdf5"] }, "chimeraviz": { "name": "chimeraviz", "version": "1.34.0", "sha256": "02y0bjlyjhh540fx3dss6lh3b7nvfv2yflmf81vsxrp24bg2y9pv", "depends": ["AnnotationDbi", "AnnotationFilter", "BiocStyle", "Biostrings", "DT", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "Gviz", "IRanges", "RCircos", "RColorBrewer", "Rgraphviz", "Rsamtools", "S4Vectors", "checkmate", "data_table", "dplyr", "ensembldb", "graph", "gtools", "magick", "org_Hs_eg_db", "org_Mm_eg_db", "plyr", "rmarkdown"] }, "chipenrich": { "name": "chipenrich", "version": "2.32.0", "sha256": "0iia6lap366dkyyql06w19gxms782wrymxhx6jv7akkp8918f071", "depends": ["AnnotationDbi", "BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "MASS", "S4Vectors", "chipenrich_data", "lattice", "latticeExtra", "mgcv", "org_Dm_eg_db", "org_Dr_eg_db", "org_Hs_eg_db", "org_Mm_eg_db", "org_Rn_eg_db", "plyr", "rms", "rtracklayer", "stringr"] }, "chipseq": { "name": "chipseq", "version": "1.58.0", "sha256": "1wav01504azcp1ghcm51nxz41nf1xz7yqfdd94yxnbfq24x9k6cw", "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "ShortRead", "lattice"] }, "chopsticks": { "name": "chopsticks", "version": "1.74.0", "sha256": "142m7732nm9h3j828kqyi1pj2w0fakryb3nampficwdfyhzdxs2r", "depends": ["survival"] }, "chromDraw": { "name": "chromDraw", "version": "2.38.0", "sha256": "00qg03dqw1j6hsih92fvdy7hxr713nkq817d4qig3k43csfbyiv4", "depends": ["GenomicRanges", "Rcpp"] }, "chromPlot": { "name": "chromPlot", "version": "1.36.0", "sha256": "09wwhk0cvmyzac9mhczrzwk78zjsdc31kl6s39fqpm17b4cm4q9c", "depends": ["GenomicRanges", "biomaRt"] }, "chromVAR": { "name": "chromVAR", "version": "1.30.1", "sha256": "1wdsq6cx3y3262kkqa3mw3m0ymja990qwzrv11vpwr22rph74qsp", "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "DT", "GenomeInfoDb", "GenomicRanges", "IRanges", "Matrix", "RColorBrewer", "Rcpp", "RcppArmadillo", "Rsamtools", "Rtsne", "S4Vectors", "SummarizedExperiment", "TFBSTools", "ggplot2", "miniUI", "nabor", "plotly", "shiny"] }, "cicero": { "name": "cicero", "version": "1.26.0", "sha256": "1vmmgvwscrag8dv5n4k70pdichfii11j2jiav3nv9l5pqby469na", "depends": ["Biobase", "BiocGenerics", "FNN", "GenomicRanges", "Gviz", "IRanges", "Matrix", "S4Vectors", "VGAM", "assertthat", "data_table", "dplyr", "ggplot2", "glasso", "igraph", "monocle", "plyr", "reshape2", "stringi", "stringr", "tibble", "tidyr"] }, "circRNAprofiler": { "name": "circRNAprofiler", "version": "1.22.1", "sha256": "0c30bzlmbfn05d6j5wvcdww5hn0mkcl9ydb4z3rf7hl58xp62s0g", "depends": ["AnnotationHub", "BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "Biostrings", "DESeq2", "GenomeInfoDb", "GenomicRanges", "IRanges", "R_utils", "S4Vectors", "dplyr", "edgeR", "ggplot2", "gwascat", "magrittr", "readr", "reshape2", "rlang", "rtracklayer", "seqinr", "stringi", "stringr", "universalmotif"] }, "cisPath": { "name": "cisPath", "version": "1.47.0", "sha256": "0q9fk47jwsbslyqjx6b4qr65xvxappr63xkvm2a6458r3hxaf41y", "depends": [] }, "cleanUpdTSeq": { "name": "cleanUpdTSeq", "version": "1.46.0", "sha256": "0nkhs4rrwpk6sxvr57ca934aknazcjlf4qx3il8l0xg7dzm2w2jl", "depends": ["BSgenome", "BSgenome_Drerio_UCSC_danRer7", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "e1071", "seqinr", "stringr"] }, "cleaver": { "name": "cleaver", "version": "1.46.0", "sha256": "0brds9xq1fywl946rbr4mqfbhvranla4vxxmk7ndma3s6hxsar7v", "depends": ["Biostrings", "IRanges", "S4Vectors"] }, "clevRvis": { "name": "clevRvis", "version": "1.8.0", "sha256": "1kshwlklcq3lhwa52bkz8alglv84xnzgcbmrxzyhwgmjnph84544", "depends": ["DT", "R_utils", "colorspace", "colourpicker", "cowplot", "dplyr", "ggiraph", "ggnewscale", "ggplot2", "ggraph", "htmlwidgets", "igraph", "magrittr", "patchwork", "purrr", "readr", "readxl", "shiny", "shinyWidgets", "shinycssloaders", "shinydashboard", "shinyhelper", "tibble"] }, "cliProfiler": { "name": "cliProfiler", "version": "1.14.0", "sha256": "1hwz4wqhh69xrfir7jlvc9bkl30g6sb5a17gq13kjn1wr901pxly", "depends": ["BSgenome", "Biostrings", "GenomicRanges", "S4Vectors", "dplyr", "ggplot2", "rtracklayer"] }, "clippda": { "name": "clippda", "version": "1.58.0", "sha256": "03fbf53cjqb4xni2y97mjla001r1g3znpj481pj9f429fmscbjhx", "depends": ["Biobase", "lattice", "limma", "rgl", "scatterplot3d", "statmod"] }, "clipper": { "name": "clipper", "version": "1.48.0", "sha256": "0r0bwvj0lagpkcidx5qffh83n9fn85wp80m2j0qrzf2bvzygmvsr", "depends": ["Biobase", "KEGGgraph", "Matrix", "Rcpp", "corpcor", "gRbase", "graph", "igraph", "qpgraph"] }, "cliqueMS": { "name": "cliqueMS", "version": "1.22.0", "sha256": "1x9wnhdfapbhrsjwd01c0ccq00zjsv2iaqw24nzmcykv89v9nv6y", "depends": ["BH", "MSnbase", "Rcpp", "RcppArmadillo", "coop", "igraph", "matrixStats", "slam", "xcms"] }, "clst": { "name": "clst", "version": "1.56.0", "sha256": "0sl6mv46r4fs8ga0s3xpqcc94y3kv1lxg1bmxwxmifqzm84bj9b4", "depends": ["ROC", "lattice"] }, "clstutils": { "name": "clstutils", "version": "1.56.0", "sha256": "1rwrgbdij8p925maspynqqjkjk5wf92dv5y9g4yhfj99d7j9fvjw", "depends": ["RSQLite", "ape", "clst", "lattice", "rjson"] }, "clustComp": { "name": "clustComp", "version": "1.36.0", "sha256": "06dw1pqf6ialfqqbiwzmvlbfm0lqzy0102gg6lcgpcxlj47b2vm1", "depends": ["sm"] }, "clustSIGNAL": { "name": "clustSIGNAL", "version": "1.0.0", "sha256": "1gibrs3bcjbc6gwp67d8xg0i6ikh91xa7iqmkcwwwc3659qlvv3i", "depends": ["BiocNeighbors", "BiocParallel", "Matrix", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "bluster", "harmony", "reshape2", "scater"] }, "clusterExperiment": { "name": "clusterExperiment", "version": "2.28.1", "sha256": "127fcfd57wfbxxxmn4gghbas2k6if1fkr777fzx2gqvq1qrd5cww", "depends": ["BiocGenerics", "BiocSingular", "DelayedArray", "HDF5Array", "Matrix", "NMF", "RColorBrewer", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "ape", "cluster", "edgeR", "kernlab", "limma", "locfdr", "matrixStats", "mbkmeans", "phylobase", "pracma", "scales", "stringr", "zinbwave"] }, "clusterProfiler": { "name": "clusterProfiler", "version": "4.16.0", "sha256": "1vgyhaisk5vx812kqyzg4kyxmn8q64i99xy9di6ds3fp84j79xyl", "depends": ["AnnotationDbi", "DOSE", "GOSemSim", "GO_db", "dplyr", "enrichplot", "gson", "httr", "igraph", "magrittr", "plyr", "qvalue", "rlang", "tidyr", "yulab_utils"] }, "clusterSeq": { "name": "clusterSeq", "version": "1.32.0", "sha256": "1klbjr2y8jymjgm4g9b680sb69n0djrclz2vqj8ca2kn36sva3dq", "depends": ["BiocGenerics", "BiocParallel", "baySeq"] }, "clusterStab": { "name": "clusterStab", "version": "1.80.0", "sha256": "1j7m5f5xhnnrpnl6f9zd23s2v6vaiywcrxliaql7sfkfkpmw9kj3", "depends": ["Biobase"] }, "clustifyr": { "name": "clustifyr", "version": "1.20.0", "sha256": "06lc9mmhiayij5hdws05h08l16z0wg6q022k301czgh0g52p0z2x", "depends": ["Matrix", "S4Vectors", "SeuratObject", "SingleCellExperiment", "SummarizedExperiment", "cowplot", "dplyr", "entropy", "fgsea", "ggplot2", "httr", "matrixStats", "proxy", "rlang", "scales", "stringr", "tibble", "tidyr"] }, "cmapR": { "name": "cmapR", "version": "1.20.0", "sha256": "036xm08qr7xxcmyvkvm4im57y1ydmhvdpbihmwgivd04q7vpalj7", "depends": ["SummarizedExperiment", "data_table", "flowCore", "matrixStats", "rhdf5"] }, "cn_farms": { "name": "cn.farms", "version": "1.56.2", "sha256": "1q35z7mywmrkibgbhaddyrk78wbnyvlkxv43bsa59bdcsbw7ns6m", "depends": ["Biobase", "DBI", "DNAcopy", "affxparser", "ff", "lattice", "oligo", "oligoClasses", "preprocessCore", "snow"] }, "cn_mops": { "name": "cn.mops", "version": "1.54.0", "sha256": "17n2pl93gijcq8cjqkjgk5w8m201f6rn0k6bh1jib42nfyx0hnl3", "depends": ["Biobase", "BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors"] }, "cnvGSA": { "name": "cnvGSA", "version": "1.52.0", "sha256": "1wl5f27mnpi3rbqisl7bl5ywvl3rzksw2zzx4faf8p11cipjzsw8", "depends": ["GenomicRanges", "brglm", "doParallel", "foreach", "splitstackshape"] }, "coGPS": { "name": "coGPS", "version": "1.52.0", "sha256": "1rd4yyv6c1qmqyr1bz1xwakys44drc62fqln6pkxn5mhxkv462zr", "depends": [] }, "coMethDMR": { "name": "coMethDMR", "version": "1.12.0", "sha256": "0qa19ccclzrxr2079avxf2j06f82dbqjyvfv69c0b45svr7hzcmf", "depends": ["AnnotationHub", "BiocParallel", "ExperimentHub", "GenomicRanges", "IRanges", "bumphunter", "lmerTest"] }, "coRdon": { "name": "coRdon", "version": "1.26.0", "sha256": "0yadnd5mc5b62jjqh3zz7si3rgwfid4r3ccxjgiqpaw6lh4a784b", "depends": ["Biobase", "Biostrings", "data_table", "dplyr", "ggplot2", "purrr", "stringr"] }, "codelink": { "name": "codelink", "version": "1.76.0", "sha256": "1bwi83n99xrys4s2ir40ngh39pdyxcp9bacpph28l8pqfb1a7mf5", "depends": ["Biobase", "BiocGenerics", "annotate", "limma"] }, "cogena": { "name": "cogena", "version": "1.42.0", "sha256": "11wncf16k393jr31qvcqlhnclavvqi9sacwr5vnlz80a23nnm38b", "depends": ["Biobase", "amap", "apcluster", "biwt", "class", "cluster", "corrplot", "devtools", "doParallel", "dplyr", "fastcluster", "foreach", "ggplot2", "gplots", "kohonen", "mclust", "reshape2", "stringr", "tibble", "tidyr"] }, "cogeqc": { "name": "cogeqc", "version": "1.12.0", "sha256": "0cmc7gqq4psl291bh81bm8nailaravnq4qbas1rpz70x1ikjx4wz", "depends": ["Biostrings", "ggbeeswarm", "ggplot2", "ggtree", "igraph", "jsonlite", "patchwork", "reshape2", "rlang", "scales"] }, "cola": { "name": "cola", "version": "2.14.0", "sha256": "0m048k36fbqardgg6qi078cc5w6fqxr3w5285nb1jc7s778sdk9j", "depends": ["BiocGenerics", "ComplexHeatmap", "GetoptLong", "GlobalOptions", "RColorBrewer", "Rcpp", "brew", "circlize", "clue", "cluster", "crayon", "digest", "doParallel", "doRNG", "eulerr", "foreach", "httr", "impute", "irlba", "knitr", "markdown", "matrixStats", "mclust", "microbenchmark", "png", "skmeans", "xml2"] }, "comapr": { "name": "comapr", "version": "1.12.0", "sha256": "0ggks950kr5c8x4l0479lh882r4svxagaq2y65hv26x23c03hzkx", "depends": ["BiocParallel", "GenomeInfoDb", "GenomicRanges", "Gviz", "IRanges", "Matrix", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "circlize", "dplyr", "foreach", "ggplot2", "gridExtra", "plotly", "plyr", "reshape2", "rlang", "scales", "tidyr"] }, "combi": { "name": "combi", "version": "1.20.0", "sha256": "08yqd9n60bh2gc0hry9y52xx7z65qrsid2ri75zy70vy33ck516r", "depends": ["BB", "Biobase", "DBI", "Matrix", "SummarizedExperiment", "alabama", "cobs", "ggplot2", "limma", "nleqslv", "phyloseq", "reshape2", "tensor", "vegan"] }, "compEpiTools": { "name": "compEpiTools", "version": "1.42.0", "sha256": "1dmsd3g4qly6s748qkq0glvad4nmfyqsp9gfyx4b31j7hc0mml49", "depends": ["AnnotationDbi", "BiocGenerics", "Biostrings", "GO_db", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "XVector", "gplots", "methylPipe", "topGO"] }, "compSPOT": { "name": "compSPOT", "version": "1.6.0", "sha256": "1b6i8kbz1c56njpldh71y7g9l0xmvcm6hjyhq2cqymdz2sdz26rs", "depends": ["data_table", "ggplot2", "ggpubr", "gridExtra", "magrittr", "plotly"] }, "compcodeR": { "name": "compcodeR", "version": "1.44.0", "sha256": "09h8yixf7559kcby4kqr6jiw5pcdr7y1lf952ai5zdjx2f7cdsvf", "depends": ["KernSmooth", "MASS", "ROCR", "ape", "caTools", "edgeR", "ggplot2", "gplots", "gtools", "knitr", "lattice", "limma", "markdown", "matrixStats", "modeest", "phylolm", "rmarkdown", "shiny", "shinydashboard", "sm", "stringr", "vioplot"] }, "concordexR": { "name": "concordexR", "version": "1.8.0", "sha256": "1l7507zk08d0idygkh4h3a281xvkrnn28wnsmpp04pq3smhabsck", "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "DelayedArray", "Matrix", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "bluster", "cli", "purrr", "rlang", "sparseMatrixStats"] }, "condiments": { "name": "condiments", "version": "1.16.0", "sha256": "13c65xq648c946nz625dl2sj2brbpbcz6wmxka6lvs29cwz7sb96", "depends": ["BiocParallel", "Ecume", "RANN", "SingleCellExperiment", "SummarizedExperiment", "TrajectoryUtils", "distinct", "dplyr", "igraph", "magrittr", "matrixStats", "mgcv", "pbapply", "slingshot"] }, "consICA": { "name": "consICA", "version": "2.6.0", "sha256": "137mkgrp95k45nh7ljv94xgf5c5ahrz1xzxq2qchrjmvh0yahwgp", "depends": ["BiocParallel", "GO_db", "Rfast", "SummarizedExperiment", "fastICA", "ggplot2", "graph", "org_Hs_eg_db", "pheatmap", "sm", "survival", "topGO"] }, "consensus": { "name": "consensus", "version": "1.26.0", "sha256": "01kh517ml7nb1qkhc8lhl4kaalfjddi3kq1pcnar0aq796vpgmby", "depends": ["RColorBrewer", "gplots", "matrixStats"] }, "consensusDE": { "name": "consensusDE", "version": "1.26.0", "sha256": "0r2agk29v5ahnp56j61gq81dradymn8v7x6cc5cnv7hvfl4bzv40", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "DESeq2", "EDASeq", "EnsDb_Hsapiens_v86", "GenomicAlignments", "GenomicFeatures", "RColorBrewer", "RUVSeq", "Rsamtools", "S4Vectors", "SummarizedExperiment", "TxDb_Dmelanogaster_UCSC_dm3_ensGene", "airway", "data_table", "dendextend", "edgeR", "ensembldb", "limma", "org_Hs_eg_db", "pcaMethods"] }, "consensusOV": { "name": "consensusOV", "version": "1.30.0", "sha256": "10zdr72admvmvcy41aa223cdc4vzbj1xklamnqvsvwxbcw9yvfms", "depends": ["Biobase", "BiocParallel", "GSVA", "gdata", "genefu", "limma", "matrixStats", "randomForest"] }, "consensusSeekeR": { "name": "consensusSeekeR", "version": "1.36.0", "sha256": "1vpkl58q4gn5wamynz0bfmhqa3zzza6fxla1qrv5wm0adrfqsm9c", "depends": ["BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "rtracklayer", "stringr"] }, "conumee": { "name": "conumee", "version": "1.42.0", "sha256": "17qqljnph3gk995prqld61b7wl3gafxpjbdylcc73wrmfqby5xd6", "depends": ["DNAcopy", "GenomeInfoDb", "GenomicRanges", "IRanges", "IlluminaHumanMethylation450kanno_ilmn12_hg19", "IlluminaHumanMethylation450kmanifest", "IlluminaHumanMethylationEPICanno_ilm10b2_hg19", "IlluminaHumanMethylationEPICmanifest", "minfi", "rtracklayer"] }, "convert": { "name": "convert", "version": "1.84.0", "sha256": "08cx9q4f588cpcc45pwvfql3sv84s3xmjs4fi00983clf8glqn38", "depends": ["Biobase", "limma", "marray"] }, "copa": { "name": "copa", "version": "1.76.0", "sha256": "0041ik9frfsz15mjsagz40rd9bs0v5lnvr6dj8xnvph1n47gyarv", "depends": ["Biobase"] }, "corral": { "name": "corral", "version": "1.18.0", "sha256": "0ax8dxpz9idb50v90m70m3qv1bm8p2iz23i90czz19iv4vzgrnid", "depends": ["Matrix", "MultiAssayExperiment", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "ggthemes", "gridExtra", "irlba", "pals", "reshape2", "transport"] }, "coseq": { "name": "coseq", "version": "1.32.1", "sha256": "1a49pzlp0gdxmg7siyl3hg5yv6mch6gqm0v14qbmac04fz6zacqd", "depends": ["BiocParallel", "DESeq2", "HTSCluster", "HTSFilter", "Rmixmod", "S4Vectors", "SummarizedExperiment", "capushe", "compositions", "corrplot", "e1071", "edgeR", "ggplot2", "mvtnorm", "scales"] }, "cosmiq": { "name": "cosmiq", "version": "1.42.0", "sha256": "0q3vprsnywlifagr5250ff7df0r72jk7ly7vgb3v11sy6bibqz0i", "depends": ["MassSpecWavelet", "Rcpp", "faahKO", "pracma", "xcms"] }, "cosmosR": { "name": "cosmosR", "version": "1.16.0", "sha256": "1wbw0cd98gvxq030s7vl7yzhap1h7i623vjsagsdmb2dc8nffhf8", "depends": ["CARNIVAL", "GSEABase", "decoupleR", "dorothea", "dplyr", "igraph", "progress", "purrr", "rlang", "stringr", "visNetwork"] }, "countsimQC": { "name": "countsimQC", "version": "1.26.0", "sha256": "0ygl54aji9gy685ylgnv5iflb82q4dmvjpy20bljld6n78mlhn86", "depends": ["DESeq2", "DT", "GenomeInfoDbData", "SummarizedExperiment", "caTools", "dplyr", "edgeR", "genefilter", "ggplot2", "ragg", "randtests", "rmarkdown", "tidyr"] }, "covEB": { "name": "covEB", "version": "1.34.0", "sha256": "1vvd43z6m3jczamz56v16siziwlap98zpfflij2k4zladbkm2qwg", "depends": ["Biobase", "LaplacesDemon", "Matrix", "gsl", "igraph", "mvtnorm"] }, "covRNA": { "name": "covRNA", "version": "1.34.0", "sha256": "11cv5q9ppki925j4ccmddv5n7224xviacvrdivzjnby94mfwmhad", "depends": ["Biobase", "ade4", "genefilter"] }, "cpvSNP": { "name": "cpvSNP", "version": "1.40.0", "sha256": "17v7h3q1b491allvwlga0irjywa0sz0c8gjwhh6gqv0f2sww71ns", "depends": ["BiocParallel", "GSEABase", "GenomicFeatures", "corpcor", "ggplot2", "plyr"] }, "cqn": { "name": "cqn", "version": "1.54.0", "sha256": "05rhs2cd9cmvn1ayn33r1ji4gjzxjym36nv6z04jy3zhac3mmzi5", "depends": ["mclust", "nor1mix", "quantreg"] }, "crisprBase": { "name": "crisprBase", "version": "1.12.0", "sha256": "1c7bjr87xr0rhmxm5wvwrl32rrh6axpmazyrm8wljzgvn3gj0v0h", "depends": ["BiocGenerics", "Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "stringr"] }, "crisprBowtie": { "name": "crisprBowtie", "version": "1.12.0", "sha256": "0hs0lawivrxjh936aq90y3c6kjmfdwl3xxqgs5pqb3za77kh73sl", "depends": ["BSgenome", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rbowtie", "crisprBase", "readr", "stringr"] }, "crisprBwa": { "name": "crisprBwa", "version": "1.12.0", "sha256": "11p6khzahab919kcvm7kyxqqww3i4n9xh2z65zj4l27hrz91crf5", "depends": ["BSgenome", "BiocGenerics", "GenomeInfoDb", "Rbwa", "crisprBase", "readr", "stringr"] }, "crisprDesign": { "name": "crisprDesign", "version": "1.10.0", "sha256": "0vfqnmsvj1xnwj2pd45c4li15nlpl1v626hhvasyklrwahsqw2qk", "depends": ["AnnotationDbi", "BSgenome", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "MatrixGenerics", "S4Vectors", "VariantAnnotation", "crisprBase", "crisprBowtie", "crisprScore", "rtracklayer", "txdbmaker"] }, "crisprScore": { "name": "crisprScore", "version": "1.12.0", "sha256": "06jwv69asw67lh6djmrax6c6dxvffr0s2dflfzvi2ld22phigwxm", "depends": ["BiocGenerics", "Biostrings", "IRanges", "XVector", "basilisk", "basilisk_utils", "crisprScoreData", "randomForest", "reticulate", "stringr"] }, "crisprShiny": { "name": "crisprShiny", "version": "1.4.0", "sha256": "0lqx31h9ixfhvvkdsw8kjjzghdb5jj7g4kbfjwv4an6z3bc4ambf", "depends": ["BSgenome", "BiocGenerics", "Biostrings", "DT", "GenomeInfoDb", "S4Vectors", "crisprBase", "crisprDesign", "crisprScore", "crisprViz", "htmlwidgets", "pwalign", "shiny", "shinyBS", "shinyjs", "waiter"] }, "crisprVerse": { "name": "crisprVerse", "version": "1.10.0", "sha256": "1cqn0wh5c4cr6ibfk1gcnkasxkyabkc1dfrci22i4fq5chz189yl", "depends": ["BiocManager", "cli", "crisprBase", "crisprBowtie", "crisprDesign", "crisprScore", "crisprScoreData", "crisprViz", "rlang"] }, "crisprViz": { "name": "crisprViz", "version": "1.10.0", "sha256": "1vdbnbnjhi7fm87kw9fdhyp248hxjp8k4d3bxiqj9iik4r926lll", "depends": ["BSgenome", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "S4Vectors", "crisprBase", "crisprDesign", "txdbmaker"] }, "crlmm": { "name": "crlmm", "version": "1.66.0", "sha256": "0nzn99xw28lr7rj3b91ca77kqmf00i4wy0bwvjy2ci0zlpdk61v3", "depends": ["Biobase", "BiocGenerics", "RcppEigen", "VGAM", "affyio", "beanplot", "ellipse", "ff", "foreach", "illuminaio", "lattice", "limma", "matrixStats", "mvtnorm", "oligoClasses", "preprocessCore"] }, "crumblr": { "name": "crumblr", "version": "1.0.0", "sha256": "1ymw4aqmj8ihagia1dh09qx19pzk1amipii1qbxpcjxcl1kx8iqv", "depends": ["MASS", "Rdpack", "Rfast", "SingleCellExperiment", "dplyr", "ggplot2", "ggtree", "tidytree", "variancePartition", "viridis"] }, "crupR": { "name": "crupR", "version": "1.0.0", "sha256": "06q1bjbrgzj1lk08v28qvpw7rz057qrdslc483ys23hwzh1yny1i", "depends": ["BiocParallel", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "TxDb_Mmusculus_UCSC_mm10_knownGene", "TxDb_Mmusculus_UCSC_mm9_knownGene", "bamsignals", "dplyr", "fs", "ggplot2", "magrittr", "matrixStats", "preprocessCore", "randomForest", "reshape2", "rtracklayer"] }, "csaw": { "name": "csaw", "version": "1.42.0", "sha256": "01mq34niz767qj91al556w1y6k7yail3bfi20y0pf5zshnn71cs9", "depends": ["BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicRanges", "IRanges", "Matrix", "Rcpp", "Rhtslib", "Rsamtools", "S4Vectors", "SummarizedExperiment", "edgeR", "limma", "metapod"] }, "csdR": { "name": "csdR", "version": "1.14.0", "sha256": "1bxip5ry510z1cvh38f63h8x3rk31cma7z0z809psclsxp74b1fw", "depends": ["Rcpp", "RhpcBLASctl", "WGCNA", "glue", "matrixStats"] }, "ctc": { "name": "ctc", "version": "1.82.0", "sha256": "0l9vncl6xk3xnywn7v1bhxmwxrrmaxmvgg0l043qzn16r2vyk4sn", "depends": ["amap"] }, "ctsGE": { "name": "ctsGE", "version": "1.34.0", "sha256": "0n3xmipmx3r51b8zhxacf47k1g20zdqg8g0wz6cpf6srvzlvqx9z", "depends": ["ccaPP", "ggplot2", "limma", "reshape2", "shiny", "stringr"] }, "cummeRbund": { "name": "cummeRbund", "version": "2.50.0", "sha256": "1i1zcrfizp4ix0bgx3gjbd4y4hj7dfs15j4ssh87kkx61y7x6yl8", "depends": ["Biobase", "BiocGenerics", "Gviz", "RSQLite", "S4Vectors", "fastcluster", "ggplot2", "plyr", "reshape2", "rtracklayer"] }, "customCMPdb": { "name": "customCMPdb", "version": "1.18.0", "sha256": "0pjv7dy0zlnqkqs3z6bgf5172bqvg1nvdip6xhkbmkyll4ai079c", "depends": ["AnnotationHub", "BiocFileCache", "ChemmineR", "RSQLite", "XML", "rappdirs"] }, "customProDB": { "name": "customProDB", "version": "1.48.0", "sha256": "1ixpq5fasq2n2f1rbwi1icnb6v96hakkv7kqsvzmp2lraxqh5lv0", "depends": ["AhoCorasickTrie", "AnnotationDbi", "Biostrings", "DBI", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "RCurl", "RSQLite", "Rsamtools", "S4Vectors", "VariantAnnotation", "biomaRt", "plyr", "rtracklayer", "stringr", "txdbmaker"] }, "cyanoFilter": { "name": "cyanoFilter", "version": "1.16.0", "sha256": "1wr1lkvv9kjzcwf3zgz76h09ga95bnzcigvp2vnc7rk0f8lz7mn0", "depends": ["Biobase", "GGally", "cytometree", "flowClust", "flowCore", "flowDensity", "ggplot2", "mrfDepth"] }, "cycle": { "name": "cycle", "version": "1.62.0", "sha256": "0q378jrqvrkm77y75fz6qjcw16njwfzlriy5249faxa0yf20xvab", "depends": ["Biobase", "Mfuzz"] }, "cydar": { "name": "cydar", "version": "1.32.1", "sha256": "0ladv04rwfhpnw54yqynh9mvc62gk3kir275xkbb35ly18zipg9p", "depends": ["Biobase", "BiocGenerics", "BiocNeighbors", "BiocParallel", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "flowCore", "shiny", "viridis"] }, "cypress": { "name": "cypress", "version": "1.4.0", "sha256": "0bvwwmaawa6xpxgfp775br5llqz82sz9wh5i3psvmwws7wsdczsn", "depends": ["BiocParallel", "DESeq2", "MASS", "PROPER", "RColorBrewer", "SummarizedExperiment", "TCA", "TOAST", "abind", "checkmate", "dplyr", "e1071", "edgeR", "mvtnorm", "preprocessCore", "rlang", "sirt", "tibble"] }, "cytoKernel": { "name": "cytoKernel", "version": "1.14.0", "sha256": "07x046cwf59jsbnwcgwpjm5wzlmm84ccgwb1ygzsg1s8b6mzim6m", "depends": ["BiocParallel", "ComplexHeatmap", "Rcpp", "S4Vectors", "SummarizedExperiment", "ashr", "circlize", "data_table", "dplyr", "magrittr", "rlang"] }, "cytoMEM": { "name": "cytoMEM", "version": "1.12.0", "sha256": "0a86434v4v8phnssaza9zn5bgplq6667s0gss2ddn23l58yyc38b", "depends": ["flowCore", "gplots", "matrixStats"] }, "cytofQC": { "name": "cytofQC", "version": "1.8.0", "sha256": "13lcf0bldkccpgz5673cn2n64wqmwx98qpb9vzdlbin981pxr5ny", "depends": ["CATALYST", "EZtune", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "e1071", "flowCore", "gbm", "ggplot2", "hrbrthemes", "matrixStats", "randomForest", "rmarkdown", "ssc"] }, "cytolib": { "name": "cytolib", "version": "2.20.0", "sha256": "1rv3dpqx6g7l6h1s6rpqipgyhhdzq6328zca1wg50kglqzdxx2a2", "depends": ["BH", "RProtoBufLib", "Rhdf5lib"] }, "cytomapper": { "name": "cytomapper", "version": "1.20.0", "sha256": "0fgd654madgnr01v9wryh8yq2aqybqnq81nl34kki37dr73avfzb", "depends": ["BiocParallel", "DelayedArray", "EBImage", "HDF5Array", "RColorBrewer", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "ggbeeswarm", "ggplot2", "matrixStats", "nnls", "raster", "rhdf5", "shiny", "shinydashboard", "svgPanZoom", "svglite", "viridis"] }, "cytoviewer": { "name": "cytoviewer", "version": "1.8.0", "sha256": "1qjmpkpy50izvb0aw92793k173hi88byny5ygna3bvv6mdf53glw", "depends": ["EBImage", "RColorBrewer", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "archive", "colourpicker", "cytomapper", "shiny", "shinycssloaders", "shinydashboard", "svgPanZoom", "svglite", "viridis"] }, "dStruct": { "name": "dStruct", "version": "1.14.0", "sha256": "0xk5qmqkdi2pb6qfmxr1mm8lwdz9bxpxw0l49lfb3zwrhp5bssm7", "depends": ["IRanges", "S4Vectors", "ggplot2", "purrr", "reshape2", "rlang", "zoo"] }, "daMA": { "name": "daMA", "version": "1.80.0", "sha256": "0f7fcawfr8glqphihbvys8grirc13b4wlziqfbdljn1hi8sh6i8w", "depends": ["MASS"] }, "dada2": { "name": "dada2", "version": "1.36.0", "sha256": "0lxva0lvh3xcpkrjalkg2ps8jlzaypnsy3ibd9mk4lnjpbn5hiii", "depends": ["BiocGenerics", "Biostrings", "IRanges", "Rcpp", "RcppParallel", "ShortRead", "XVector", "ggplot2", "reshape2"] }, "dagLogo": { "name": "dagLogo", "version": "1.46.0", "sha256": "12pbxddfxwcd7izamzqjiac0vm4572lv4ghn39zysb9j8fbbjscm", "depends": ["BiocGenerics", "Biostrings", "UniProt_ws", "biomaRt", "httr", "motifStack", "pheatmap"] }, "dandelionR": { "name": "dandelionR", "version": "1.0.2", "sha256": "0m8p003mgf03n69z0bcbid2insskg04vhhrvrppsciqcc9a4rbb4", "depends": ["BiocGenerics", "MASS", "Matrix", "RANN", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "bluster", "destiny", "igraph", "miloR", "purrr", "rlang", "spam", "uwot"] }, "dar": { "name": "dar", "version": "1.4.0", "sha256": "1yxvfk4dp4hpb90qkgwj7b4g79ydzykpxapwd1lvzk0iqa7f2nyx", "depends": ["ComplexHeatmap", "UpSetR", "cli", "crayon", "dplyr", "generics", "ggplot2", "glue", "gplots", "heatmaply", "magrittr", "mia", "phyloseq", "purrr", "readr", "rlang", "scales", "stringr", "tibble", "tidyr", "waldo"] }, "dcGSA": { "name": "dcGSA", "version": "1.36.0", "sha256": "0gpa7z68rrb7w866l3v37sx3i048r1jj42bxws26w8aldf6bzc7x", "depends": ["BiocParallel", "Matrix"] }, "dcanr": { "name": "dcanr", "version": "1.24.0", "sha256": "1cmc40d8mbxh79pwwbqqwhbvmfib08asp04r2wi2gi24n80aw1im", "depends": ["Matrix", "RColorBrewer", "circlize", "doRNG", "foreach", "igraph", "plyr", "reshape2", "stringr"] }, "dce": { "name": "dce", "version": "1.13.0", "sha256": "02gnlskfgn38fcf5mchp6ippcd2rj4cl4w7r08igaqyl02zy2x80", "depends": ["MASS", "Matrix", "Rgraphviz", "assertthat", "dplyr", "edgeR", "epiNEM", "expm", "ggplot2", "ggraph", "glm2", "glue", "graph", "graphite", "harmonicmeanp", "igraph", "logger", "magrittr", "metap", "mnem", "naturalsort", "org_Hs_eg_db", "pcalg", "ppcor", "purrr", "reshape2", "rlang", "shadowtext", "tidygraph", "tidyverse"] }, "ddCt": { "name": "ddCt", "version": "1.64.0", "sha256": "0qprpc9l6nzxlb66kq0zkylypc2ljjndbl5z70hpsy5vq5dwy1bv", "depends": ["Biobase", "BiocGenerics", "RColorBrewer", "lattice", "xtable"] }, "ddPCRclust": { "name": "ddPCRclust", "version": "1.28.0", "sha256": "0ky64kfan378xk4akjab7rh6s4bmghr2cdy8bvr07ihszbz3qrik", "depends": ["R_utils", "SamSPECTRAL", "clue", "flowCore", "flowDensity", "flowPeaks", "ggplot2", "openxlsx", "plotrix"] }, "dearseq": { "name": "dearseq", "version": "1.20.0", "sha256": "0as6dwgrxqshyid36435njkjvcjdasfrbl4lxgdm7yg930qr5al2", "depends": ["CompQuadForm", "KernSmooth", "dplyr", "ggplot2", "magrittr", "matrixStats", "patchwork", "pbapply", "reshape2", "rlang", "scattermore", "statmod", "survey", "tibble", "viridisLite"] }, "debCAM": { "name": "debCAM", "version": "1.26.0", "sha256": "1sh8vbhgrkk1xfk139jxi88s2z70pnr4ji2pnb2gb3s5013zrhk8", "depends": ["Biobase", "BiocParallel", "NMF", "SummarizedExperiment", "apcluster", "corpcor", "geometry", "nnls", "pcaPP", "rJava"] }, "debrowser": { "name": "debrowser", "version": "1.36.0", "sha256": "1p1r6hy8mamjvazg8cnz0v9i38fg15jnzndbm3707qa6caz5w7cz", "depends": ["AnnotationDbi", "DESeq2", "DOSE", "DT", "GenomicRanges", "Harman", "IRanges", "RColorBrewer", "RCurl", "S4Vectors", "SummarizedExperiment", "annotate", "apeglm", "ashr", "clusterProfiler", "colourpicker", "edgeR", "enrichplot", "ggplot2", "gplots", "heatmaply", "igraph", "jsonlite", "limma", "org_Hs_eg_db", "org_Mm_eg_db", "pathview", "plotly", "reshape2", "shiny", "shinyBS", "shinydashboard", "shinyjs", "stringi", "sva"] }, "decompTumor2Sig": { "name": "decompTumor2Sig", "version": "2.24.0", "sha256": "13rhg8hcraiqkdyyj85maj5zk37wlx7n5m046r9s8l4cm1pmvgqp", "depends": ["BSgenome_Hsapiens_UCSC_hg19", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "Matrix", "S4Vectors", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg19_knownGene", "VariantAnnotation", "data_table", "ggplot2", "ggseqlogo", "gridExtra", "plyr", "quadprog", "readxl"] }, "decontX": { "name": "decontX", "version": "1.6.0", "sha256": "0yar28k3nk3xxx067iflza2zyl6c59k7s04515jmz3i6l9hyh764", "depends": ["BH", "DelayedArray", "MCMCprecision", "Matrix", "Rcpp", "RcppEigen", "RcppParallel", "S4Vectors", "Seurat", "SingleCellExperiment", "StanHeaders", "SummarizedExperiment", "celda", "dbscan", "ggplot2", "patchwork", "plyr", "reshape2", "rstan", "rstantools", "scater", "withr"] }, "decontam": { "name": "decontam", "version": "1.28.0", "sha256": "1xn071m88gd2dzqkz6avdwj04lwngfhmmx3v6rwn8dp7lmqlpxyb", "depends": ["ggplot2", "reshape2"] }, "deconvR": { "name": "deconvR", "version": "1.14.2", "sha256": "04s0g9p2dvcq2pin9j80pqcrmbfvvajj6s3d000sd2afa7b5rpb2", "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "MASS", "S4Vectors", "assertthat", "data_table", "dplyr", "e1071", "foreach", "magrittr", "matrixStats", "methylKit", "minfi", "nnls", "quadprog", "rsq", "tidyr"] }, "decoupleR": { "name": "decoupleR", "version": "2.14.0", "sha256": "00sx949jgnagil55miqb2mzq8bqfn8l44w761qwh7rs4xs83m33a", "depends": ["BiocParallel", "Matrix", "broom", "dplyr", "magrittr", "parallelly", "purrr", "rlang", "stringr", "tibble", "tidyr", "tidyselect", "withr"] }, "deepSNV": { "name": "deepSNV", "version": "1.54.0", "sha256": "04m9k8gq7iv45srg8sa778dpc15qiq98rr9j3n1y5z11ghj15ijw", "depends": ["Biostrings", "GenomicRanges", "IRanges", "Rhtslib", "SummarizedExperiment", "VGAM", "VariantAnnotation"] }, "deltaCaptureC": { "name": "deltaCaptureC", "version": "1.22.0", "sha256": "14qvbxbab930x4399vx64wz4l5bmspdj4kb7bmx8m1c0a2rwflws", "depends": ["DESeq2", "GenomicRanges", "IRanges", "SummarizedExperiment", "ggplot2", "tictoc"] }, "deltaGseg": { "name": "deltaGseg", "version": "1.48.0", "sha256": "0xdm81wb0pmz9rcplfrc7px47hlaqv3kf92idvn3ldm46z4jlw4a", "depends": ["changepoint", "fBasics", "ggplot2", "pvclust", "reshape", "scales", "tseries", "wavethresh"] }, "demuxSNP": { "name": "demuxSNP", "version": "1.6.0", "sha256": "02gnqd5myn8j4003hmyawaym43yb571dacd0i2np8sfzldc1v67m", "depends": ["BiocGenerics", "GenomeInfoDb", "IRanges", "KernelKnn", "Matrix", "MatrixGenerics", "SingleCellExperiment", "SummarizedExperiment", "VariantAnnotation", "class", "demuxmix", "dplyr", "ensembldb"] }, "demuxmix": { "name": "demuxmix", "version": "1.10.0", "sha256": "1vdgalqwn1gflhabf9aqzb591gakaq0yh6ddic9l79awj1i04266", "depends": ["MASS", "Matrix", "ggplot2", "gridExtra"] }, "densvis": { "name": "densvis", "version": "1.18.0", "sha256": "10finfm8fr0pvl6gnv9q90x3xlyccn2mbka4y08vjiyq50mzgla6", "depends": ["Rcpp", "Rtsne", "assertthat", "basilisk", "irlba", "reticulate"] }, "derfinder": { "name": "derfinder", "version": "1.42.0", "sha256": "083y2qsy1ix7ikz8ppf4b49ya4ipf18sxc3gznisybx807nsk4zs", "depends": ["AnnotationDbi", "BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicFiles", "GenomicRanges", "Hmisc", "IRanges", "Rsamtools", "S4Vectors", "bumphunter", "derfinderHelper", "qvalue", "rtracklayer"] }, "derfinderHelper": { "name": "derfinderHelper", "version": "1.42.0", "sha256": "1sww441lkk6i24a8cxamwwfa64lgdgsv57h1sq605bsswml9ird0", "depends": ["IRanges", "Matrix", "S4Vectors"] }, "derfinderPlot": { "name": "derfinderPlot", "version": "1.42.0", "sha256": "12sjwmjj9b61m6baa24ghg6iy0f87yq32km1rr59j5mmjmdhmrj1", "depends": ["GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "derfinder", "ggbio", "ggplot2", "limma", "plyr", "reshape2", "scales"] }, "destiny": { "name": "destiny", "version": "3.22.0", "sha256": "01l01b6k55ifhppsp83scjf3f168r62xigz73s718ik8qbvirgqa", "depends": ["Biobase", "BiocGenerics", "Matrix", "RSpectra", "Rcpp", "RcppEigen", "RcppHNSW", "SingleCellExperiment", "SummarizedExperiment", "VIM", "ggplot2", "ggplot_multistats", "ggthemes", "irlba", "knn_covertree", "pcaMethods", "proxy", "rlang", "scales", "scatterplot3d", "smoother", "tidyr", "tidyselect"] }, "diffGeneAnalysis": { "name": "diffGeneAnalysis", "version": "1.90.0", "sha256": "0vsbl4g5rq5dg1l3n3kapfwl9bmrxibdrm39hcjjh0rf7w5kfd3k", "depends": ["minpack_lm"] }, "diffHic": { "name": "diffHic", "version": "1.40.0", "sha256": "0yanl7awdxk9z4gxv48df9qpniwqmfalp4fisfac1yabrs681266", "depends": ["BSgenome", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "InteractionSet", "Rcpp", "Rhtslib", "Rsamtools", "S4Vectors", "SummarizedExperiment", "csaw", "edgeR", "limma", "locfit", "rhdf5", "rtracklayer"] }, "diffUTR": { "name": "diffUTR", "version": "1.16.0", "sha256": "0srj0jv7kq5zs87k3d4s6h94mfbg9gdb2p98rhyyrx9bc36ijcqi", "depends": ["ComplexHeatmap", "DEXSeq", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rsubread", "S4Vectors", "SummarizedExperiment", "dplyr", "edgeR", "ensembldb", "ggplot2", "ggrepel", "limma", "matrixStats", "rtracklayer", "stringi", "viridisLite"] }, "diffcoexp": { "name": "diffcoexp", "version": "1.28.0", "sha256": "0gx8c3wsdzx7yh9sqykvh346lk47xw8zph50x1j5jrkqbnvrahws", "depends": ["BiocGenerics", "DiffCorr", "SummarizedExperiment", "WGCNA", "igraph", "psych"] }, "diffcyt": { "name": "diffcyt", "version": "1.28.0", "sha256": "16z53ghrvv3rc1c6bbw9n8yywfzvl1bzzm0h3axhqzk0r8mlzgj8", "depends": ["ComplexHeatmap", "FlowSOM", "S4Vectors", "SummarizedExperiment", "circlize", "dplyr", "edgeR", "flowCore", "limma", "lme4", "magrittr", "multcomp", "reshape2", "tidyr"] }, "diffuStats": { "name": "diffuStats", "version": "1.28.0", "sha256": "0plyan6dyp19ssba30k5giafg18h92by1vmfzncknjykj1sb3r9q", "depends": ["MASS", "Matrix", "Rcpp", "RcppArmadillo", "RcppParallel", "checkmate", "expm", "igraph", "plyr", "precrec"] }, "diggit": { "name": "diggit", "version": "1.40.0", "sha256": "19cg56s0aw2vnw8yg94l9zpg69q4cpmmqvdmh1wa31g0cg1rwsrw", "depends": ["Biobase", "ks", "viper"] }, "dinoR": { "name": "dinoR", "version": "1.4.0", "sha256": "1ys0jygld8jz06lh3lpa9cvmda8cc80da791fvg1fjklvg0p1zjh", "depends": ["BiocGenerics", "ComplexHeatmap", "GenomicRanges", "Matrix", "SummarizedExperiment", "circlize", "cowplot", "dplyr", "edgeR", "ggplot2", "rlang", "stringr", "tibble", "tidyr", "tidyselect"] }, "dir_expiry": { "name": "dir.expiry", "version": "1.16.0", "sha256": "09hsmml075v0ccynq6mps24frjf79mj8nl7xbzykglvwbjbs9h7f", "depends": ["filelock"] }, "discordant": { "name": "discordant", "version": "1.32.0", "sha256": "1gjqxjypv323pa9klbhax61i884n5rdvzgwxnqbhbam6vzcid6vv", "depends": ["Biobase", "MASS", "Rcpp", "biwt", "dplyr", "gtools"] }, "distinct": { "name": "distinct", "version": "1.20.0", "sha256": "09qccx43sj7pcffh8gbi7213iyz8paxh6z70lff0dv0zs9nza8k7", "depends": ["Matrix", "Rcpp", "RcppArmadillo", "SingleCellExperiment", "SummarizedExperiment", "doParallel", "doRNG", "foreach", "ggplot2", "limma", "scater"] }, "dittoSeq": { "name": "dittoSeq", "version": "1.20.0", "sha256": "013m2fhczxmq1jk05fjyih2aphaqylpmvfby7z8wk91g51221q48", "depends": ["S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "colorspace", "cowplot", "ggplot2", "ggrepel", "ggridges", "gridExtra", "pheatmap", "reshape2"] }, "divergence": { "name": "divergence", "version": "1.24.0", "sha256": "0vzv741qxkjkq8l5xq53qlrdr7mjq2qlacpddr0w8b6sc6kjblh4", "depends": ["SummarizedExperiment"] }, "dks": { "name": "dks", "version": "1.54.0", "sha256": "1vibsj07rqix1b6dbgzv2z30jkv39mfqq1pajvxb99pb1q7gm009", "depends": ["cubature"] }, "dmrseq": { "name": "dmrseq", "version": "1.28.0", "sha256": "0zqp8nn3qhw7ds5y34apy3cwi6mb2kj8ywkkml26m5jyc613hj9i", "depends": ["AnnotationHub", "BiocParallel", "DelayedMatrixStats", "GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "annotatr", "bsseq", "bumphunter", "ggplot2", "locfit", "matrixStats", "nlme", "outliers", "rtracklayer"] }, "dominoSignal": { "name": "dominoSignal", "version": "1.2.0", "sha256": "02bsz2nd6yjybhnkna8ixhchq0hvbkhm0jz5cfbddyvgyqg5f7ix", "depends": ["ComplexHeatmap", "Matrix", "biomaRt", "circlize", "dplyr", "ggpubr", "igraph", "magrittr", "plyr", "purrr"] }, "doppelgangR": { "name": "doppelgangR", "version": "1.36.1", "sha256": "0cd4n5p5sh5pnszwb5vy28m722vk7i0xdkn86ki6jcrv528f3ijc", "depends": ["Biobase", "BiocParallel", "SummarizedExperiment", "digest", "impute", "mnormt", "sva"] }, "doseR": { "name": "doseR", "version": "1.24.0", "sha256": "0h6m4z9lk32xxy14dcrvpvwfsg574qgyfa89smrjxcnccsn3rck6", "depends": ["RUnit", "S4Vectors", "SummarizedExperiment", "digest", "edgeR", "lme4", "matrixStats", "mclust"] }, "doubletrouble": { "name": "doubletrouble", "version": "1.8.1", "sha256": "1a08sd6a56h75km9y306a7gfhlnv5m2zzs1kaixwqk2v2lfvq6g2", "depends": ["AnnotationDbi", "Biostrings", "GenomicFeatures", "GenomicRanges", "MSA2dist", "ggplot2", "mclust", "rlang", "syntenet"] }, "drawProteins": { "name": "drawProteins", "version": "1.28.0", "sha256": "06fv2fhka123kj9rc2h0z07ym30wxk24fq8v0pzmf8gfyg4ywgfj", "depends": ["dplyr", "ggplot2", "httr", "readr", "tidyr"] }, "dreamlet": { "name": "dreamlet", "version": "1.6.0", "sha256": "0cp6iwdkp399nzj3a7gmyak6y5v2kzkvhqcm7rrj047pxyjb7yc8", "depends": ["BiocGenerics", "BiocParallel", "DelayedArray", "DelayedMatrixStats", "GSEABase", "IRanges", "MASS", "Matrix", "MatrixGenerics", "Rcpp", "Rdpack", "S4Arrays", "S4Vectors", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "ashr", "beachmat", "broom", "data_table", "dplyr", "edgeR", "ggbeeswarm", "ggplot2", "ggrepel", "gtools", "irlba", "limma", "lme4", "mashr", "metafor", "purrr", "remaCor", "reshape2", "rlang", "scattermore", "sparseMatrixStats", "tidyr", "variancePartition", "zenith"] }, "drugTargetInteractions": { "name": "drugTargetInteractions", "version": "1.16.0", "sha256": "129bdb7aaf16az9nms0qv4akgqjkqvrn95g8m6c311c44f9a9rvs", "depends": ["AnnotationFilter", "BiocFileCache", "RSQLite", "S4Vectors", "UniProt_ws", "biomaRt", "dplyr", "ensembldb", "rappdirs"] }, "dupRadar": { "name": "dupRadar", "version": "1.38.0", "sha256": "1r9n8fjb2spkvdaqbzpa50dn6cv9l995ljn4ac52ypr2z920nph1", "depends": ["KernSmooth", "Rsubread"] }, "dyebias": { "name": "dyebias", "version": "1.68.0", "sha256": "0r42siraii99pvac7za1383c12pl1i2i2x4n64ca6rkyjqfpzqm6", "depends": ["Biobase", "marray"] }, "easier": { "name": "easier", "version": "1.14.0", "sha256": "1kdnglx6ixnff36vbpl01qv2y8kg61h936dx2qmqsqlyyc2id0n0", "depends": ["BiocParallel", "DESeq2", "ROCR", "coin", "decoupleR", "dorothea", "dplyr", "easierData", "ggplot2", "ggpubr", "ggrepel", "magrittr", "matrixStats", "progeny", "quantiseqr", "reshape2", "rlang", "rstatix", "tibble", "tidyr"] }, "easyRNASeq": { "name": "easyRNASeq", "version": "2.44.0", "sha256": "09nw3afdri5ypdmn5jb7s3pi3a4yv40f4ajh53wnsvsav47c7zla", "depends": ["Biobase", "BiocFileCache", "BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "LSD", "Rsamtools", "S4Vectors", "ShortRead", "SummarizedExperiment", "biomaRt", "edgeR", "genomeIntervals", "rappdirs"] }, "easylift": { "name": "easylift", "version": "1.6.0", "sha256": "1d07dmrcivw9z7sv274apbdkk2bi282j2ky3xxngzhjwvlq2lpxq", "depends": ["BiocFileCache", "GenomeInfoDb", "GenomicRanges", "R_utils", "rtracklayer"] }, "easyreporting": { "name": "easyreporting", "version": "1.20.0", "sha256": "1bjhqy7i6f4ymab22n23i6wyx1v1swlprkbxrldfwp9fqaqzn6ji", "depends": ["rlang", "rmarkdown", "shiny"] }, "ecolitk": { "name": "ecolitk", "version": "1.80.0", "sha256": "1mv4jp1gwhbcill3zcwalh146jz052dfxcsklvwd91v2x5n0d49f", "depends": ["Biobase"] }, "edge": { "name": "edge", "version": "2.40.0", "sha256": "0a4hlr3j4wwichiad40mvgdb6zs9ss0ap1qyjhjwbrbndlyjw0cd", "depends": ["Biobase", "MASS", "qvalue", "sva"] }, "edgeR": { "name": "edgeR", "version": "4.6.3", "sha256": "139vnp9dgpw02nbpa69bcl7jx3nw16l0w2gj3ljq4cgk5amwdplk", "depends": ["limma", "locfit"] }, "eds": { "name": "eds", "version": "1.10.0", "sha256": "1a2wk6v9vx1zzwd7h71n1dqb4a0s7d0igmzp2fdb5sbscxshpgsr", "depends": ["Matrix", "Rcpp"] }, "eiR": { "name": "eiR", "version": "1.48.0", "sha256": "0j9015icchzcgks55jpmix4xkxhrwfgc20vgblbv5c85h26mqhsk", "depends": ["BiocGenerics", "ChemmineR", "DBI", "RCurl", "RUnit", "RcppAnnoy", "digest", "snow", "snowfall"] }, "eisaR": { "name": "eisaR", "version": "1.20.0", "sha256": "1hhi2lbmja6xbcxzjplaarsslc1jvim1v1yr1skmknl8fq6zbzz5", "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "edgeR", "limma"] }, "enhancerHomologSearch": { "name": "enhancerHomologSearch", "version": "1.14.0", "sha256": "0i2aiq4q9lypyn0sgz6s1mbmw6hah0zffzmyp008hz82m86a8xpp", "depends": ["BSgenome", "BiocFileCache", "BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "Matrix", "Rcpp", "S4Vectors", "httr", "jsonlite", "motifmatchr", "pwalign", "rtracklayer"] }, "enrichViewNet": { "name": "enrichViewNet", "version": "1.6.1", "sha256": "0qi63zwn78506gryf438w3fdcv0m98v4db5v6wv44f35r74s1khv", "depends": ["DOSE", "RCy3", "enrichplot", "gprofiler2", "jsonlite", "strex", "stringr"] }, "enrichplot": { "name": "enrichplot", "version": "1.28.4", "sha256": "0wlhx0djh3by2949y7gmjjiscgh7mdvzm2al7p81vxjrgaw221k7", "depends": ["DOSE", "GOSemSim", "RColorBrewer", "aplot", "ggfun", "ggnewscale", "ggplot2", "ggrepel", "ggtangle", "ggtree", "igraph", "magrittr", "plyr", "purrr", "reshape2", "rlang", "scatterpie", "yulab_utils"] }, "ensembldb": { "name": "ensembldb", "version": "2.32.0", "sha256": "0h7jhryn6f3gdr2189nm7d18n6kh7wgh95l93ng1rs1n20vsn1a4", "depends": ["AnnotationDbi", "AnnotationFilter", "Biobase", "BiocGenerics", "Biostrings", "DBI", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "ProtGenerics", "RSQLite", "Rsamtools", "S4Vectors", "curl", "rtracklayer"] }, "epiNEM": { "name": "epiNEM", "version": "1.32.0", "sha256": "1mgdvfiq5lxp5j18b91rnaqjiqaxksm6g15crq0ivjllkad4564g", "depends": ["BoolNet", "BoutrosLab_plotting_general", "RColorBrewer", "e1071", "graph", "gtools", "igraph", "latex2exp", "lattice", "latticeExtra", "minet", "mnem", "pcalg"] }, "epialleleR": { "name": "epialleleR", "version": "1.16.0", "sha256": "0qac87i0jfiz73m3npbqk77yzn2vv7b7p0bfpmhh57zc6xgg90c9", "depends": ["BH", "BiocGenerics", "GenomicRanges", "Rcpp", "Rhtslib", "data_table"] }, "epidecodeR": { "name": "epidecodeR", "version": "1.16.0", "sha256": "0xamhd0zjx935v7lg009anfkrdrjhdbfskji4ngs05mq793m816y", "depends": ["EnvStats", "GenomicRanges", "IRanges", "dplyr", "ggplot2", "ggpubr", "rstatix", "rtracklayer"] }, "epigenomix": { "name": "epigenomix", "version": "1.48.1", "sha256": "05wvdfrgj2hpj8qm83k6jfbl4794zcafsh1g0d9bzd882f1n43bs", "depends": ["Biobase", "BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "MCMCpack", "Rsamtools", "S4Vectors", "SummarizedExperiment", "beadarray"] }, "epigraHMM": { "name": "epigraHMM", "version": "1.16.0", "sha256": "0b7ya0psb89fw3l575zc5jljrkpqmxgqx9wvn5sivgldfagl8ji8", "depends": ["GenomeInfoDb", "GenomicRanges", "GreyListChIP", "IRanges", "MASS", "Matrix", "Rcpp", "RcppArmadillo", "Rhdf5lib", "Rsamtools", "S4Vectors", "SummarizedExperiment", "bamsignals", "csaw", "data_table", "ggplot2", "ggpubr", "limma", "magrittr", "pheatmap", "rhdf5", "rtracklayer", "scales"] }, "epimutacions": { "name": "epimutacions", "version": "1.12.0", "sha256": "1sv2vjpg4bdky9vjph6g6hpgmzhzk5142dbxmw26dwh5k4ix45xj", "depends": ["AnnotationDbi", "AnnotationHub", "BiocGenerics", "BiocParallel", "ExperimentHub", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "Gviz", "Homo_sapiens", "IRanges", "IlluminaHumanMethylation450kanno_ilmn12_hg19", "IlluminaHumanMethylation450kmanifest", "IlluminaHumanMethylationEPICanno_ilm10b2_hg19", "IlluminaHumanMethylationEPICmanifest", "S4Vectors", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg18_knownGene", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "biomaRt", "bumphunter", "ensembldb", "epimutacionsData", "ggplot2", "ggrepel", "gridExtra", "isotree", "matrixStats", "minfi", "purrr", "reshape2", "robustbase", "rtracklayer", "tibble"] }, "epiregulon": { "name": "epiregulon", "version": "1.4.0", "sha256": "0kcbck56myl79npnsqapgsg2i5zxrlyd1j10qpr7i1dq41gjpqsm", "depends": ["AUCell", "AnnotationHub", "BSgenome_Hsapiens_UCSC_hg19", "BSgenome_Hsapiens_UCSC_hg38", "BSgenome_Mmusculus_UCSC_mm10", "BiocParallel", "ExperimentHub", "GenomeInfoDb", "GenomicRanges", "IRanges", "Matrix", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "assorthead", "beachmat", "bluster", "checkmate", "entropy", "lifecycle", "motifmatchr", "scMultiome", "scran", "scuttle"] }, "epiregulon_extra": { "name": "epiregulon.extra", "version": "1.4.0", "sha256": "08mc1awkvhknsb5x8w7c4s0p8a1jhdcs8yygk1n93pw48n2vkb3c", "depends": ["ComplexHeatmap", "Matrix", "SingleCellExperiment", "SummarizedExperiment", "checkmate", "circlize", "clusterProfiler", "ggplot2", "ggraph", "igraph", "patchwork", "reshape2", "scales", "scater", "scran"] }, "epistack": { "name": "epistack", "version": "1.14.0", "sha256": "1yr12p2xr39a4jjpfw5y605wsdh7sbmiwsfj0yjlyzxvjp48nkpj", "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "plotrix"] }, "epistasisGA": { "name": "epistasisGA", "version": "1.10.0", "sha256": "18sg3csw8pp2zmvp2ly9ff2hfa7p5igs81sjmzqlhglcn08nll9w", "depends": ["BH", "BiocParallel", "Rcpp", "RcppArmadillo", "batchtools", "bigmemory", "data_table", "ggplot2", "igraph", "matrixStats", "qgraph", "survival"] }, "epivizr": { "name": "epivizr", "version": "2.38.0", "sha256": "0bj5wps73b5lxh9k8jkhyhprsfaifc4g6jllrzahlgdxy7yknj81", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "bumphunter", "epivizrData", "epivizrServer"] }, "epivizrChart": { "name": "epivizrChart", "version": "1.30.0", "sha256": "0i2d7bxzz5mmdy9mkzw98mdj9bicycj4xz9flh29yavwg35kgwy7", "depends": ["BiocGenerics", "epivizrData", "epivizrServer", "htmltools", "rjson"] }, "epivizrData": { "name": "epivizrData", "version": "1.36.0", "sha256": "11m31lik07blzigb2z7skzapk7yn6n26gy4h20qh8dq2l6ijvqdc", "depends": ["Biobase", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "OrganismDbi", "S4Vectors", "SummarizedExperiment", "ensembldb", "epivizrServer"] }, "epivizrServer": { "name": "epivizrServer", "version": "1.36.0", "sha256": "12faax9c502yxd4k0dflcwgg7n2lydai6r65nr76pw4qs6pgczvp", "depends": ["R6", "httpuv", "mime", "rjson"] }, "epivizrStandalone": { "name": "epivizrStandalone", "version": "1.36.0", "sha256": "0i8hzjj0d5pzrnz8w9y13k7awmxaf1ns28bkw34l41vb7yy46vap", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicFeatures", "S4Vectors", "epivizr", "epivizrServer", "git2r"] }, "erccdashboard": { "name": "erccdashboard", "version": "1.42.0", "sha256": "103xyw11mij3yk0p3z4cd697pl2lxkfzh2blysdz2py4glc9m49w", "depends": ["MASS", "ROCR", "edgeR", "ggplot2", "gplots", "gridExtra", "gtools", "knitr", "limma", "locfit", "plyr", "qvalue", "reshape2", "scales", "stringr"] }, "erma": { "name": "erma", "version": "1.24.1", "sha256": "1s3b2a0iv3rl3sxq1sbqscq2h2gjz4d3vsg9phhnbk1xdhbhqi4d", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicFiles", "GenomicRanges", "Homo_sapiens", "IRanges", "S4Vectors", "SummarizedExperiment", "ggplot2", "rtracklayer", "shiny"] }, "esATAC": { "name": "esATAC", "version": "1.30.0", "sha256": "09hwn5j2grjn4qhjwdvs2nj7cm68bx8j1v47jbpkpf0mhyvdjibq", "depends": ["AnnotationDbi", "BSgenome", "BiocGenerics", "BiocManager", "Biostrings", "ChIPseeker", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "JASPAR2018", "R_utils", "Rbowtie2", "Rcpp", "Rsamtools", "S4Vectors", "ShortRead", "TFBSTools", "VennDiagram", "clusterProfiler", "corrplot", "digest", "ggplot2", "igraph", "knitr", "magrittr", "motifmatchr", "pipeFrame", "rJava", "rmarkdown", "rtracklayer"] }, "escape": { "name": "escape", "version": "2.4.0", "sha256": "1vwahi1c89jhdnnfk2z2pf1aa5h4sd5a66kgyzx30z907x2bc37a", "depends": ["AUCell", "BiocParallel", "GSEABase", "GSVA", "Matrix", "MatrixGenerics", "SeuratObject", "SingleCellExperiment", "SummarizedExperiment", "UCell", "dplyr", "ggdist", "ggplot2", "ggpointdensity", "ggridges", "msigdb", "patchwork", "reshape2", "stringr"] }, "escheR": { "name": "escheR", "version": "1.8.0", "sha256": "10wx02wjmjyw22y7pk4jpm3j6bizrq33yl5ikbnf629vgav3qfaj", "depends": ["SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "ggplot2", "rlang"] }, "esetVis": { "name": "esetVis", "version": "1.34.0", "sha256": "0ssnbq8gib94w7s8x88a80nmpw050kz4m39d3shxdvi6vbz7ms39", "depends": ["Biobase", "MASS", "MLP", "Rtsne", "hexbin", "mpm"] }, "eudysbiome": { "name": "eudysbiome", "version": "1.38.0", "sha256": "02spdv3dvkj6b0zhsyq481jrijmsrcpkr6xvf0g2d6b68bmkghj8", "depends": ["Biostrings", "R_utils", "Rsamtools", "plyr"] }, "evaluomeR": { "name": "evaluomeR", "version": "1.24.0", "sha256": "0dagpwlnbqhc3xya7l4xwr1c44mg9c88ck94rq6rr9psi1y05k8r", "depends": ["MASS", "MultiAssayExperiment", "RSKC", "Rdpack", "SummarizedExperiment", "class", "cluster", "corrplot", "dendextend", "dplyr", "flexmix", "fpc", "ggdendro", "ggplot2", "kableExtra", "matrixStats", "mclust", "plotrix", "prabclus", "randomForest", "reshape2", "sparcl"] }, "extraChIPs": { "name": "extraChIPs", "version": "1.12.0", "sha256": "0gc9w6qccnncdlnn1vgc6nfiwhv865z2788cq9f3pmsgj80s0d7y", "depends": ["BiocParallel", "GenomeInfoDb", "GenomicRanges", "IRanges", "InteractionSet", "RColorBrewer", "Rsamtools", "S4Vectors", "SummarizedExperiment", "csaw", "dplyr", "edgeR", "forcats", "ggplot2", "ggrepel", "ggside", "glue", "matrixStats", "patchwork", "rlang", "rtracklayer", "scales", "stringr", "tibble", "tidyr", "tidyselect", "vctrs"] }, "fCCAC": { "name": "fCCAC", "version": "1.34.0", "sha256": "0jbwdilz3vr4gpxn21q24kz44f3bdx3vf37ydkaaz10n3pbdsw7a", "depends": ["ComplexHeatmap", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "fda", "genomation", "ggplot2"] }, "fCI": { "name": "fCI", "version": "1.38.0", "sha256": "07npq64gmbaql37879d5kh2y5wqf56a7d22241qfmhjm799z1ggv", "depends": ["FNN", "VennDiagram", "gtools", "psych", "rgl", "zoo"] }, "fabia": { "name": "fabia", "version": "2.54.0", "sha256": "1jvpqvd6cfs3id1cgjjbg7ifmzzkca3xkdbwb8rr9sm7lwfbcfs1", "depends": ["Biobase"] }, "factDesign": { "name": "factDesign", "version": "1.84.0", "sha256": "11v6hhmkyq9saibw9fhv9m2ppdk8mxyhkrhnzy7w3fbd7z18gpf3", "depends": ["Biobase"] }, "factR": { "name": "factR", "version": "1.10.0", "sha256": "131rmjl1awazpapmdag3kcjxjgb5gdxh2xvrvpvzhw45r4nd69v0", "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RCurl", "S4Vectors", "XML", "crayon", "data_table", "dplyr", "drawProteins", "ggplot2", "pbapply", "purrr", "rlang", "rtracklayer", "stringr", "tibble", "tidyr", "wiggleplotr"] }, "faers": { "name": "faers", "version": "1.4.0", "sha256": "0snz9sd3pdcid1dws1j8x1hipxvphqqk98j8xap3arr17jq764c0", "depends": ["BiocParallel", "MCMCpack", "brio", "cli", "curl", "data_table", "httr2", "openEBGM", "rlang", "rvest", "vroom", "xml2"] }, "famat": { "name": "famat", "version": "1.18.0", "sha256": "00fzbqa065z2si0yq4gvici4vfxwa8dwfyx077kc9d7a4z99b2wa", "depends": ["BiasedUrn", "DT", "GO_db", "KEGGREST", "clusterProfiler", "dplyr", "gprofiler2", "magrittr", "mgcv", "ontologyIndex", "org_Hs_eg_db", "plotly", "rWikiPathways", "reactome_db", "shiny", "shinyBS", "shinydashboard", "stringr", "tidyr"] }, "fastLiquidAssociation": { "name": "fastLiquidAssociation", "version": "1.44.0", "sha256": "1dp8z0541h63267h2p9zfiarfn44k9nnz3k2af2xb276r36wllri", "depends": ["Hmisc", "LiquidAssociation", "WGCNA", "doParallel", "impute", "preprocessCore"] }, "fastreeR": { "name": "fastreeR", "version": "1.12.5", "sha256": "1ydbj10aksv1amkh7wpz76g1kx0r947qz4gxxindic8wk4kilcsn", "depends": ["R_utils", "ape", "data_table", "dynamicTreeCut", "rJava", "stringr"] }, "fastseg": { "name": "fastseg", "version": "1.54.0", "sha256": "04cshbi1jl730fs2dszzh9whviffp3bga6h6cxjxx6d9zr55l6za", "depends": ["Biobase", "BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors"] }, "fcScan": { "name": "fcScan", "version": "1.22.0", "sha256": "1sby20vm6pkrq3wwk9yhkp488w5m79mfdn0bbwnqfhlqhjacvpiy", "depends": ["GenomicRanges", "IRanges", "SummarizedExperiment", "VariantAnnotation", "doParallel", "foreach", "plyr", "rtracklayer"] }, "fdrame": { "name": "fdrame", "version": "1.80.0", "sha256": "185d9isf0vrmhknxabhfic8jwr4jalxjmj9y0fnn67kc1ysf9nbf", "depends": [] }, "fedup": { "name": "fedup", "version": "1.16.0", "sha256": "1aip4v07xvbcb7q9r248hsgqzgpbb3apda3x39gc168q2jamf5yd", "depends": ["RColorBrewer", "RCy3", "data_table", "dplyr", "forcats", "ggplot2", "ggthemes", "openxlsx", "tibble"] }, "fenr": { "name": "fenr", "version": "1.6.1", "sha256": "0drvdhi8zynnx7h77mlfkxf7sqw8hydz8ni7sz1zvs920s8x4h5h", "depends": ["BiocFileCache", "assertthat", "dplyr", "ggplot2", "httr2", "progress", "purrr", "readr", "rlang", "rvest", "shiny", "stringr", "tibble", "tidyr", "tidyselect"] }, "ffpe": { "name": "ffpe", "version": "1.52.0", "sha256": "1pgb6vga9id08zk4bw23sfn93asnvk2ardl3vc09dgb1414q8mvd", "depends": ["Biobase", "BiocGenerics", "TTR", "affy", "lumi", "methylumi", "sfsmisc"] }, "fgga": { "name": "fgga", "version": "1.16.0", "sha256": "1p6h1fg8x9d7v07sb48sqwshdxnk0zmb9nzq5c4g467dlpsn4zig", "depends": ["BiocFileCache", "RBGL", "curl", "e1071", "gRbase", "graph", "igraph", "jsonlite"] }, "fgsea": { "name": "fgsea", "version": "1.34.2", "sha256": "1wq3n3pqjmcf8zj8cj5fkkyz5mf4ii656qj7vbny6vf46jl7bq5f", "depends": ["BH", "BiocParallel", "Matrix", "Rcpp", "cowplot", "data_table", "fastmatch", "ggplot2", "scales"] }, "findIPs": { "name": "findIPs", "version": "1.4.0", "sha256": "14zbzv9pxnz3g04v7c9cvn277n53qc4agyq6n4p7rdbl1jwy40p4", "depends": ["Biobase", "BiocParallel", "SummarizedExperiment", "survival"] }, "fishpond": { "name": "fishpond", "version": "2.14.0", "sha256": "140p6xk45awb1a6x3d2am2mqn4m33fs5f8qpp5wdfl8arzvm38j9", "depends": ["GenomicRanges", "IRanges", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "abind", "gtools", "jsonlite", "matrixStats", "qvalue", "svMisc"] }, "flagme": { "name": "flagme", "version": "1.64.0", "sha256": "0jvhjycnyzw7bny4wka3kws4ka5yrzmhmm3k3h4k6gvihmvhzzsf", "depends": ["CAMERA", "MASS", "SparseM", "gcspikelite", "gplots", "xcms"] }, "flowAI": { "name": "flowAI", "version": "1.38.0", "sha256": "1w28hcfychhws8s5vkv27zssyvngrsrflnqc12y7f895f3lp72s1", "depends": ["RColorBrewer", "changepoint", "flowCore", "ggplot2", "knitr", "plyr", "reshape2", "rmarkdown", "scales"] }, "flowBeads": { "name": "flowBeads", "version": "1.46.0", "sha256": "16vici8l03lnssxmdhl5lq36mk40yd0sxmr9j8jmkm6spmkz813k", "depends": ["Biobase", "flowCore", "knitr", "rrcov", "xtable"] }, "flowBin": { "name": "flowBin", "version": "1.44.0", "sha256": "1b2rb9fci6p4nsp0a8m11hhghhd2fzvqbnykvm5dq0h0vm3i5sx1", "depends": ["BiocGenerics", "class", "flowCore", "flowFP", "limma", "snow"] }, "flowCHIC": { "name": "flowCHIC", "version": "1.42.0", "sha256": "096br2ryviv69yr8av7k35d60z7c4pdgb0kaywhxjprk7iwjqhfy", "depends": ["EBImage", "flowCore", "ggplot2", "hexbin", "vegan"] }, "flowClean": { "name": "flowClean", "version": "1.46.0", "sha256": "0m5la5r8qg3hbf5yhl0vinxncxjx44cvlj6f0kdpg542vkwp6bnz", "depends": ["bit", "changepoint", "flowCore", "sfsmisc"] }, "flowClust": { "name": "flowClust", "version": "3.46.0", "sha256": "04zmgp11fajl72kif74zy3974dg780hx9dwp3g7y6dywf5bihlg6", "depends": ["Biobase", "BiocGenerics", "flowCore", "graph"] }, "flowCore": { "name": "flowCore", "version": "2.20.0", "sha256": "15px1dc2z9vlvnh0kyg3l74bwmhnb22bpyzrsxi2bvx61lf3bzgp", "depends": ["BH", "Biobase", "BiocGenerics", "RProtoBufLib", "Rcpp", "S4Vectors", "cpp11", "cytolib", "matrixStats"] }, "flowCut": { "name": "flowCut", "version": "1.18.0", "sha256": "0afdqildijv1rhhqwrnk4jqxq70y1vmm1ys1hpl6q9y2wig5ak03", "depends": ["Cairo", "e1071", "flowCore", "flowDensity"] }, "flowCyBar": { "name": "flowCyBar", "version": "1.44.0", "sha256": "0n42kdyw6318nij1c4dzdfkaf6rma92hjmsydcs2aqw7fy99s8w8", "depends": ["gplots", "vegan"] }, "flowDensity": { "name": "flowDensity", "version": "1.42.0", "sha256": "0dwxl44aichngdsnyx33cxbhla7wv4zp6gx92xqryjmdfh375ic4", "depends": ["car", "flowCore", "flowViz", "gplots", "polyclip"] }, "flowFP": { "name": "flowFP", "version": "1.66.0", "sha256": "04p1zwb0d8yz966fpyaiaydhzylh5di1gfa29mvvba39kfjqy7ch", "depends": ["Biobase", "BiocGenerics", "flowCore", "flowViz"] }, "flowGate": { "name": "flowGate", "version": "1.8.0", "sha256": "0wjgi20xina1d8xna4qg46r3m7ixns092pq2zpn90cgcvl05wa62", "depends": ["BiocManager", "dplyr", "flowCore", "flowWorkspace", "ggcyto", "ggplot2", "purrr", "rlang", "shiny", "tibble"] }, "flowGraph": { "name": "flowGraph", "version": "1.16.0", "sha256": "0x0q08rf89wscxzanqn6sw32bmdbk63y6m77ad82zr5zbc36hckj", "depends": ["Matrix", "Rdpack", "data_table", "effsize", "furrr", "future", "ggiraph", "ggplot2", "ggrepel", "gridExtra", "htmlwidgets", "igraph", "matrixStats", "purrr", "stringi", "stringr", "visNetwork"] }, "flowMatch": { "name": "flowMatch", "version": "1.44.0", "sha256": "037lak2axxjjp2g79z1casfyrrpl7vjlyk70k5q1fmx2747b50rm", "depends": ["Biobase", "Rcpp", "flowCore"] }, "flowMeans": { "name": "flowMeans", "version": "1.68.0", "sha256": "1jg9q3b0jkiiycd0zsc2jgmfdasrml8c9ri61bjmm7ps0wiq92il", "depends": ["Biobase", "feature", "flowCore", "rrcov"] }, "flowMerge": { "name": "flowMerge", "version": "2.56.0", "sha256": "1b925163l0dkzjhrpbrxc35yndr4n6vicdpzk6qzigdw9fxw2k9v", "depends": ["Rgraphviz", "feature", "flowClust", "flowCore", "foreach", "graph", "rrcov", "snow"] }, "flowPeaks": { "name": "flowPeaks", "version": "1.54.0", "sha256": "1dcd2h2jspiq1qh207mbajizsqbxlnrmn2927fwpshhckbkjkgm3", "depends": [] }, "flowPloidy": { "name": "flowPloidy", "version": "1.34.0", "sha256": "1nc4cly3by1qkdy2z24knlpw0k7n7d7j2p19xvg1nrh7znky5vwx", "depends": ["caTools", "car", "flowCore", "knitr", "minpack_lm", "rmarkdown", "shiny"] }, "flowPlots": { "name": "flowPlots", "version": "1.56.0", "sha256": "1b91pg78cby4da211ilgvs7flqwr77f9awpnrpg8d0rn1vb2qsz4", "depends": [] }, "flowSpecs": { "name": "flowSpecs", "version": "1.22.0", "sha256": "1c1224gyw3rxhcsllg4z9lcy6v87j3lr3hmgv1yj0ihlmp9d7c12", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "flowCore", "ggplot2", "reshape2", "zoo"] }, "flowStats": { "name": "flowStats", "version": "4.20.0", "sha256": "1dm5aqycdabw3q2pxvpwf1hhzsplyx4b9xw1pgc2h0wk2fvdr2qc", "depends": ["Biobase", "BiocGenerics", "KernSmooth", "MASS", "RColorBrewer", "clue", "cluster", "corpcor", "fda", "flowCore", "flowViz", "flowWorkspace", "ks", "lattice", "mnormt", "ncdfFlow", "rrcov"] }, "flowTime": { "name": "flowTime", "version": "1.32.0", "sha256": "1l9w8hxahbjm8x620hqyqiryj53ml9ffrq6ihf2v4sxalxz93vnp", "depends": ["dplyr", "flowCore", "magrittr", "plyr", "rlang", "tibble"] }, "flowTrans": { "name": "flowTrans", "version": "1.60.0", "sha256": "0b9mfrbhr2dj31ck35ypzlynci9vbnk52mpfz7m5r3pjganlpfln", "depends": ["flowClust", "flowCore", "flowViz"] }, "flowVS": { "name": "flowVS", "version": "1.40.0", "sha256": "0p20bcbz67dwk51xwhrxdzj64v7p852xmhihihyzxp1fq7s4k0rs", "depends": ["flowCore", "flowStats", "flowViz"] }, "flowViz": { "name": "flowViz", "version": "1.72.0", "sha256": "135n5p1maz6622pw81dgsqzsz675x5gwq3mghp4w6jbgiyjjphmj", "depends": ["Biobase", "IDPmisc", "KernSmooth", "MASS", "RColorBrewer", "flowCore", "hexbin", "lattice", "latticeExtra"] }, "flowWorkspace": { "name": "flowWorkspace", "version": "4.20.0", "sha256": "1jrbi87zy11ls40d0c9gmdfd9ab53182ip3brg1gvgnr6sz930vx", "depends": ["BH", "Biobase", "BiocGenerics", "DelayedArray", "RBGL", "RProtoBufLib", "Rgraphviz", "Rhdf5lib", "S4Vectors", "XML", "cpp11", "cytolib", "data_table", "dplyr", "flowCore", "ggplot2", "graph", "matrixStats", "ncdfFlow", "scales"] }, "flowcatchR": { "name": "flowcatchR", "version": "1.42.0", "sha256": "069j7xw0hkyg3c45gra8wlz76msngby2iga3q390m5kiwa9z7za4", "depends": ["BiocParallel", "EBImage", "abind", "colorRamps", "plotly", "shiny"] }, "fmcsR": { "name": "fmcsR", "version": "1.50.0", "sha256": "0js75zd5hp53lvmlidj14mb28mj7mvy34mmwvn2md5na41dns5ny", "depends": ["BiocGenerics", "ChemmineR", "RUnit"] }, "fmrs": { "name": "fmrs", "version": "1.18.0", "sha256": "1p1c4gfm7w676pfqhq9z0d9m5k5mbzdvnsjh8mwxv75a0sa0fdvx", "depends": ["survival"] }, "fobitools": { "name": "fobitools", "version": "1.16.0", "sha256": "18mwca5hh95dhbkgwc4ginmy67amh8dl62zyxa2np2wxl9wsqafg", "depends": ["RecordLinkage", "clisymbols", "crayon", "dplyr", "fgsea", "ggplot2", "ggraph", "magrittr", "ontologyIndex", "purrr", "stringr", "textclean", "tictoc", "tidygraph", "tidyr", "vroom"] }, "frenchFISH": { "name": "frenchFISH", "version": "1.20.0", "sha256": "1l6ikm1k176h8qqh8hjd5hk39p6wbh46l08kn64srfwrin0m1jxg", "depends": ["MCMCpack", "NHPoisson"] }, "frma": { "name": "frma", "version": "1.60.0", "sha256": "00ln0hzlmja4i9vd6h3sjyp3k0lz4hpd2kn56j9gqgja7f0npj79", "depends": ["Biobase", "BiocGenerics", "DBI", "MASS", "affy", "oligo", "oligoClasses", "preprocessCore"] }, "frmaTools": { "name": "frmaTools", "version": "1.60.0", "sha256": "1iilympv6mmyjldw0lr3qcj8bv6i2g6dpvwbb5a9k6dd52p4mrzi", "depends": ["Biobase", "DBI", "affy", "preprocessCore"] }, "funOmics": { "name": "funOmics", "version": "1.2.0", "sha256": "0c3666b01skpvj1wfwk3l4rgkfbmrw60q5b92wxzd79gp322kqi6", "depends": ["AnnotationDbi", "KEGGREST", "NMF", "dplyr", "org_Hs_eg_db", "pathifier", "stringr"] }, "funtooNorm": { "name": "funtooNorm", "version": "1.32.0", "sha256": "1mfsr7p0x6khha29js0y3jj1w447f3p9fsxi1kyx8gp7pd1bdmv3", "depends": ["GenomeInfoDb", "IlluminaHumanMethylation450kanno_ilmn12_hg19", "IlluminaHumanMethylation450kmanifest", "matrixStats", "minfi", "pls"] }, "gCrisprTools": { "name": "gCrisprTools", "version": "2.14.0", "sha256": "0vmwd6hz1w5gfbkzc1isizxqy77dlxly71lqr92qvzykv9b59zk1", "depends": ["Biobase", "ComplexHeatmap", "RobustRankAggreg", "SummarizedExperiment", "ggplot2", "limma", "rmarkdown"] }, "gDNAx": { "name": "gDNAx", "version": "1.6.1", "sha256": "0cnpgrsy8xz6xr8adyynlxwzkipd88035802albvyxlmms3jhr9v", "depends": ["AnnotationDbi", "AnnotationHub", "BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicFiles", "GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "SummarizedExperiment", "bitops", "cli", "matrixStats", "plotrix"] }, "gDR": { "name": "gDR", "version": "1.6.0", "sha256": "0pd05qqn49qs4n2lx3rn6pqyqifyc2012p4ba1vgsky77y5jhz12", "depends": ["gDRcore", "gDRimport", "gDRutils"] }, "gDRcore": { "name": "gDRcore", "version": "1.6.0", "sha256": "02zja1gslhvhdqs48nlm71c5bzbzl1lmlkpgqgqj4yws2n0drv42", "depends": ["BiocParallel", "BumpyMatrix", "MultiAssayExperiment", "S4Vectors", "SummarizedExperiment", "checkmate", "data_table", "futile_logger", "gDRutils", "purrr", "stringr"] }, "gDRimport": { "name": "gDRimport", "version": "1.6.0", "sha256": "09ww37jgwl77njf9m89sb769f05da4mvnj2kkdxan7x9wjdsxyxq", "depends": ["BumpyMatrix", "CoreGx", "MultiAssayExperiment", "PharmacoGx", "S4Vectors", "SummarizedExperiment", "XML", "assertthat", "checkmate", "data_table", "futile_logger", "gDRutils", "magrittr", "openxlsx", "readxl", "rio", "stringi", "tibble", "yaml"] }, "gDRstyle": { "name": "gDRstyle", "version": "1.6.0", "sha256": "1xbjfn0sk9jn4q8652dbg6wd0xg9n75i8gyrdf2kzv0xrgwwcmcm", "depends": ["BiocCheck", "BiocManager", "BiocStyle", "checkmate", "desc", "git2r", "lintr", "pkgbuild", "rcmdcheck", "remotes", "rjson", "withr", "yaml"] }, "gDRutils": { "name": "gDRutils", "version": "1.6.0", "sha256": "099l59gm0g7q6rnhbp9vyimaw17blp65krp40z2r1nxd6rglr0k0", "depends": ["BiocParallel", "BumpyMatrix", "MultiAssayExperiment", "S4Vectors", "SummarizedExperiment", "checkmate", "data_table", "drc", "jsonlite", "jsonvalidate", "stringr"] }, "gINTomics": { "name": "gINTomics", "version": "1.4.0", "sha256": "04b1ksazr3l1b1k5rylmswzlfgz5xixgds2n10a1yiqwbbcjkn2p", "depends": ["AnnotationDbi", "BiocGenerics", "BiocParallel", "ComplexHeatmap", "DT", "GenomicFeatures", "GenomicRanges", "InteractiveComplexHeatmap", "MASS", "MethylMix", "MultiAssayExperiment", "OmnipathR", "RColorBrewer", "ReactomePA", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg38_knownGene", "TxDb_Mmusculus_UCSC_mm10_knownGene", "biomaRt", "callr", "circlize", "clusterProfiler", "dplyr", "edgeR", "ggplot2", "ggridges", "ggtree", "ggvenn", "gtools", "limma", "org_Hs_eg_db", "org_Mm_eg_db", "plotly", "plyr", "randomForest", "reshape2", "shiny", "shiny_gosling", "shinydashboard", "shinyjs", "stringi", "stringr", "visNetwork"] }, "gaga": { "name": "gaga", "version": "2.54.0", "sha256": "1nx98853d9waqxx7vh64fxxp4704jk443l8vbfvsypbqhk5qd5bb", "depends": ["Biobase", "EBarrays", "coda", "mgcv"] }, "gage": { "name": "gage", "version": "2.58.0", "sha256": "0fnc53iplws7qwx3hg66b9im8g50bsb7v22dkhd8xvrsgbnn0ydr", "depends": ["AnnotationDbi", "GO_db", "KEGGREST", "graph"] }, "garfield": { "name": "garfield", "version": "1.36.0", "sha256": "0ri0iay0rmckfb59sanch9df9k65bwwvpvaa95vb7wyjsp0fzsmn", "depends": [] }, "gatom": { "name": "gatom", "version": "1.6.0", "sha256": "0a8r9k2aly0lhb9yfq0sc4pmgkrgycgsgcdi1nh3izj34w1q953h", "depends": ["BioNet", "GGally", "XML", "data_table", "ggplot2", "htmltools", "htmlwidgets", "igraph", "intergraph", "mwcsr", "network", "plyr", "pryr", "shinyCyJS", "sna"] }, "gcapc": { "name": "gcapc", "version": "1.32.0", "sha256": "056cwamgjf43nkd5sbp5dya78a11x7v54bl6g9c7mh9p8pccjwk3", "depends": ["BSgenome", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "MASS", "Rsamtools", "S4Vectors", "matrixStats"] }, "gcatest": { "name": "gcatest", "version": "2.8.0", "sha256": "1cwc9sshjzv3brasvc9ka30zmg8nrmkwz5ab61bgkx43a28f9ddh", "depends": ["lfa"] }, "gcrma": { "name": "gcrma", "version": "2.80.0", "sha256": "0c49gwx1jdvp2kb58iwlvxr0j2yav04hc7v4gkbvmdc77fk8bslm", "depends": ["Biobase", "BiocManager", "Biostrings", "XVector", "affy", "affyio"] }, "gdsfmt": { "name": "gdsfmt", "version": "1.44.1", "sha256": "0xyhjlpasrncyjz3hh3lx8midy52z1b6dp59bv383wa621fb0j0b", "depends": [] }, "geNetClassifier": { "name": "geNetClassifier", "version": "1.48.0", "sha256": "1x2q78nvinrj7j72z12cl9jx2cv3klpq7hrqr2r7jianjw6prhqc", "depends": ["Biobase", "EBarrays", "e1071", "minet"] }, "gemini": { "name": "gemini", "version": "1.22.0", "sha256": "0c2g357j9kap9fs5s4yd0jvwdinvlbj41q1rcyzibbw22b7gi6li", "depends": ["dplyr", "ggplot2", "magrittr", "mixtools", "pbmcapply", "scales"] }, "gemma_R": { "name": "gemma.R", "version": "3.4.5", "sha256": "00n90ysznnx3gv6j6646f7wjjfia56ig4d2qayq058shxwdcays3", "depends": ["Biobase", "R_utils", "S4Vectors", "SummarizedExperiment", "assertthat", "base64enc", "bit64", "data_table", "digest", "glue", "httr", "jsonlite", "kableExtra", "lubridate", "magrittr", "memoise", "rappdirs", "rlang", "stringr", "tibble", "tidyr"] }, "genArise": { "name": "genArise", "version": "1.84.0", "sha256": "1yaq0ka093wml2z5xpxkq34s28ry9yh2as4dpkgc6wjd4cw4jy2c", "depends": ["locfit", "tkrplot", "xtable"] }, "geneAttribution": { "name": "geneAttribution", "version": "1.34.0", "sha256": "0i1whgj0n1n92ciw0iha9xf4pwapf8hfgn4nw2yn3x0jq5cm2id5", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "org_Hs_eg_db", "rtracklayer"] }, "geneClassifiers": { "name": "geneClassifiers", "version": "1.32.0", "sha256": "0gckcfsjciia99qaxpy32i2brdsswkxdvgf5idl34a4dd775qj1z", "depends": ["Biobase", "BiocGenerics"] }, "geneRecommender": { "name": "geneRecommender", "version": "1.80.0", "sha256": "0yz81hdxcx1q41am5i3m5dvzpmzjh12ahjibk6z2m2srpyx52a9n", "depends": ["Biobase"] }, "geneRxCluster": { "name": "geneRxCluster", "version": "1.44.0", "sha256": "1d5r41y5wgza7jmjhcmyzk5zsnby9x12r2cb7fw4xrmycmmr3f56", "depends": ["GenomicRanges", "IRanges"] }, "geneXtendeR": { "name": "geneXtendeR", "version": "1.34.0", "sha256": "19biavls97s80zhxcl0dhyw6x7jawhxgvvjkasspimzryj34944f", "depends": ["AnnotationDbi", "BiocStyle", "GO_db", "RColorBrewer", "SnowballC", "data_table", "dplyr", "networkD3", "org_Rn_eg_db", "rtracklayer", "tm", "wordcloud"] }, "genefilter": { "name": "genefilter", "version": "1.90.0", "sha256": "0zdwa8sm91fpmnmq2r726a8ihmwg8k7pi17v9cwv7bvimlkzngnc", "depends": ["AnnotationDbi", "Biobase", "MatrixGenerics", "annotate", "survival"] }, "genefu": { "name": "genefu", "version": "2.40.0", "sha256": "0cxxlyk3grc2kjagnlmxc7svbq1qkq4572c2zlmkjhcf62abci1b", "depends": ["AIMS", "amap", "biomaRt", "iC10", "iC10TrainingData", "impute", "limma", "mclust", "survcomp"] }, "geneplast": { "name": "geneplast", "version": "1.34.0", "sha256": "1la7h15w3d8v4b297r772spff301kbr51jib6a952rg10knsi897", "depends": ["ape", "data_table", "igraph", "snow"] }, "geneplotter": { "name": "geneplotter", "version": "1.86.0", "sha256": "13a8rn620d56wwfi0zskqxm2dkv65ly6xfv512gymcglxc359d95", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "RColorBrewer", "annotate", "lattice"] }, "genoCN": { "name": "genoCN", "version": "1.59.0", "sha256": "1fyyq6759p7pz8ajgkn08clpvygm8b25jlf8m3sgrvw62kwcilxl", "depends": [] }, "genomation": { "name": "genomation", "version": "1.40.1", "sha256": "1rjxh2vwkiadqprsn6d67nd3nllxy2f5g0xakxnfv6p4ry8fccfs", "depends": ["BSgenome", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rcpp", "Rsamtools", "S4Vectors", "data_table", "ggplot2", "gridBase", "impute", "matrixStats", "plotrix", "plyr", "readr", "reshape2", "rtracklayer", "seqPattern"] }, "genomeIntervals": { "name": "genomeIntervals", "version": "1.64.0", "sha256": "1zahjzxi8m9kv9g2g9dxs4fmhcmvwcvksa4js3zzfyrbgx7j517l", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "intervals"] }, "genomes": { "name": "genomes", "version": "3.38.0", "sha256": "1ix8nlwz1q88i1qfl60nsii355k98garnz4zzh3gnmjfd5drypdp", "depends": ["curl", "readr"] }, "genomicInstability": { "name": "genomicInstability", "version": "1.14.0", "sha256": "05f30zqj331qiphfdl6vr9zb075jzxpkmzrs9dblqh5b7m198j1l", "depends": ["SummarizedExperiment", "checkmate", "mixtools"] }, "geomeTriD": { "name": "geomeTriD", "version": "1.2.0", "sha256": "02a1jy2p04ls17j453xf211pr7fq0a9nfg3m4710dfiyl0dx4h14", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "InteractionSet", "MASS", "Matrix", "RANN", "S4Vectors", "dbscan", "htmlwidgets", "igraph", "plotrix", "rgl", "rjson", "scales", "trackViewer"] }, "gep2pep": { "name": "gep2pep", "version": "1.28.0", "sha256": "10lxc4qlkc8brcd4wvp0s27b2hvja5aygfyw8rnpl83a1zy7ayvg", "depends": ["Biobase", "GSEABase", "XML", "digest", "foreach", "iterators", "repo", "rhdf5"] }, "getDEE2": { "name": "getDEE2", "version": "1.18.0", "sha256": "1d134sw87gianypnymgkwqr5pqq7rrnqwml43mglpnk4jrx8xgpi", "depends": ["SummarizedExperiment", "htm2txt"] }, "geva": { "name": "geva", "version": "1.16.0", "sha256": "1lwacqif40xj636y8qvbm40jgiw1hf3avp1frchcacbxr2fxg6ki", "depends": ["dbscan", "fastcluster", "matrixStats"] }, "geyser": { "name": "geyser", "version": "1.0.0", "sha256": "04s28nbrlgwc0v59dpakmvb823qvz62lbiz2hg98b46l7cb6lwq9", "depends": ["BiocStyle", "ComplexHeatmap", "DT", "SummarizedExperiment", "bslib", "dplyr", "ggbeeswarm", "ggplot2", "htmltools", "magrittr", "shiny", "tibble", "tidyr", "tidyselect"] }, "gg4way": { "name": "gg4way", "version": "1.6.1", "sha256": "1hlriz5hr31dn62dld1f6cg6dbr0gbahq7aavy4shchgbsnj6cji", "depends": ["DESeq2", "dplyr", "edgeR", "ggplot2", "ggrepel", "glue", "janitor", "limma", "magrittr", "purrr", "rlang", "scales", "stringr", "tibble", "tidyr"] }, "ggbio": { "name": "ggbio", "version": "1.56.0", "sha256": "1vdnwcq90awh2g48xirgsha07w33kqvi73mz6f3c6896abmz7p9w", "depends": ["AnnotationDbi", "AnnotationFilter", "BSgenome", "Biobase", "BiocGenerics", "Biostrings", "GGally", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Hmisc", "IRanges", "OrganismDbi", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "biovizBase", "ensembldb", "ggplot2", "gridExtra", "gtable", "reshape2", "rlang", "rtracklayer", "scales"] }, "ggcyto": { "name": "ggcyto", "version": "1.36.0", "sha256": "0pdbp05vv9n7dal1bmdkvb0p9vb4lixk19wr2k93kpj3bkc0dzaz", "depends": ["RColorBrewer", "data_table", "flowCore", "flowWorkspace", "ggplot2", "gridExtra", "hexbin", "ncdfFlow", "plyr", "rlang", "scales"] }, "ggkegg": { "name": "ggkegg", "version": "1.6.0", "sha256": "1cqg5inir80vwhzzd3jc7xs4j4nc7yy0lkiql6qviivrv0zs3yqj", "depends": ["BiocFileCache", "XML", "data_table", "dplyr", "ggplot2", "ggraph", "gtable", "igraph", "magick", "patchwork", "shadowtext", "stringr", "tibble", "tidygraph"] }, "ggmanh": { "name": "ggmanh", "version": "1.12.0", "sha256": "1kig1r2lbnkvs5y4xcs1z4m2gvkfly27bjf8ahpvbij6yyvgmydj", "depends": ["RColorBrewer", "SeqArray", "dplyr", "gdsfmt", "ggplot2", "ggrepel", "magrittr", "paletteer", "pals", "rlang", "scales", "tidyr"] }, "ggmsa": { "name": "ggmsa", "version": "1.14.1", "sha256": "0abaqsxv9b2bniw74dg0nwianxi76z8mlnnjjlrfdbxivph9ccyw", "depends": ["Biostrings", "R4RNA", "RColorBrewer", "aplot", "dplyr", "ggforce", "ggfun", "ggplot2", "ggtree", "magrittr", "seqmagick", "tidyr"] }, "ggsc": { "name": "ggsc", "version": "1.6.1", "sha256": "0avni6b37snrpw9jldzmibklrz52jp46j680w8pgprbasfy27313", "depends": ["RColorBrewer", "Rcpp", "RcppArmadillo", "RcppParallel", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "cli", "dplyr", "ggfun", "ggplot2", "rlang", "scales", "scattermore", "tibble", "tidydr", "tidyr", "yulab_utils"] }, "ggseqalign": { "name": "ggseqalign", "version": "1.2.0", "sha256": "0k3p0rj5kx7rl35wrxzq334gkfls5bhx5j6lvn53j4snncipd2r1", "depends": ["dplyr", "ggplot2", "pwalign"] }, "ggspavis": { "name": "ggspavis", "version": "1.14.3", "sha256": "1fi54ndrlxpmwyrxq790nad781rjzb0v2ja398af58fhyqgrqzpz", "depends": ["RColorBrewer", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "ggplot2", "ggrepel", "ggside", "scales"] }, "ggtree": { "name": "ggtree", "version": "3.16.3", "sha256": "06ij3l921vazzcv07jbggsv1mb9ikgqfwhc9g20yjz7y0xcgmclj", "depends": ["ape", "aplot", "cli", "dplyr", "ggfun", "ggplot2", "magrittr", "purrr", "rlang", "scales", "tidyr", "tidytree", "treeio", "yulab_utils"] }, "ggtreeDendro": { "name": "ggtreeDendro", "version": "1.10.0", "sha256": "0jg2604wib9mdq88avmzndbjymhhzg0l9ig6j1hlv9fcgv62n2q1", "depends": ["ggplot2", "ggtree", "tidytree"] }, "ggtreeExtra": { "name": "ggtreeExtra", "version": "1.18.0", "sha256": "1dp6is7sqz88lbcxjn0khw6qm5szqad74yr0jbv3axd025nv2rp5", "depends": ["cli", "ggnewscale", "ggplot2", "ggtree", "magrittr", "rlang", "tidytree"] }, "ggtreeSpace": { "name": "ggtreeSpace", "version": "1.4.0", "sha256": "0imkzs139xr8385cn6629xa6ral87w8w522rb4jfqglkiykf9zrh", "depends": ["GGally", "ape", "dplyr", "ggplot2", "ggtree", "interp", "phytools", "rlang", "tibble", "tidyr", "tidyselect"] }, "ginmappeR": { "name": "ginmappeR", "version": "1.4.0", "sha256": "0a93nllavx3jpyr233p2qr72560mglkc2if657xlr99j7237z2bm", "depends": ["KEGGREST", "UniProt_ws", "XML", "cachem", "httr", "jsonlite", "memoise", "rentrez", "rvest"] }, "girafe": { "name": "girafe", "version": "1.60.0", "sha256": "06cfbmr8y8xi3z3dl92w0ljl6w4px2m9nr28yp71i9yswa39j107", "depends": ["Biobase", "BiocGenerics", "Biostrings", "IRanges", "Rsamtools", "S4Vectors", "ShortRead", "genomeIntervals", "intervals", "pwalign"] }, "glmGamPoi": { "name": "glmGamPoi", "version": "1.20.0", "sha256": "0mfwhlj3mli7c5iabd90gbdzc22cvqq2wh26l3bqxjv5im07hgmx", "depends": ["BiocGenerics", "DelayedArray", "DelayedMatrixStats", "HDF5Array", "Matrix", "MatrixGenerics", "Rcpp", "RcppArmadillo", "S4Vectors", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "assorthead", "beachmat", "matrixStats", "rlang", "vctrs"] }, "glmSparseNet": { "name": "glmSparseNet", "version": "1.26.0", "sha256": "1fai7mkh4rspc2k7n09wwbxq03ap0d67ij3zwlbda2gfr997c88b", "depends": ["Matrix", "MultiAssayExperiment", "SummarizedExperiment", "TCGAutils", "biomaRt", "checkmate", "dplyr", "forcats", "futile_logger", "ggplot2", "glmnet", "glue", "httr", "lifecycle", "readr", "rlang", "survminer"] }, "globalSeq": { "name": "globalSeq", "version": "1.36.0", "sha256": "1vpdrbbx82hr467dns4fgkjx3bm2hkp9w69xnb9ji74d8pzpcnj7", "depends": [] }, "globaltest": { "name": "globaltest", "version": "5.62.0", "sha256": "0ra53iisn0ccb4l5icwrzrdkk4vzhpkr1pz2i7gi4iryyxlzbgf5", "depends": ["AnnotationDbi", "Biobase", "annotate", "survival"] }, "gmapR": { "name": "gmapR", "version": "1.50.0", "sha256": "0y2bw13vmnh752vakcnaqqwgx4sf1vkizcn1km98s1c8p10c45dv", "depends": ["BSgenome", "Biobase", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "VariantAnnotation", "rtracklayer"] }, "gmoviz": { "name": "gmoviz", "version": "1.20.0", "sha256": "0kbw83sif16g4316m1hb16426xv7wch4wj2ggiyi6srd445d1ykj", "depends": ["BiocGenerics", "Biostrings", "ComplexHeatmap", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "circlize", "colorspace", "gridBase", "pracma", "rtracklayer"] }, "goProfiles": { "name": "goProfiles", "version": "1.70.0", "sha256": "06fgri975nnqad5mdppfara2w7fhpy0w8jfakz4mbg5n80spk770", "depends": ["AnnotationDbi", "Biobase", "CompQuadForm", "GO_db", "stringr"] }, "goSTAG": { "name": "goSTAG", "version": "1.32.0", "sha256": "1zp6lgxcy8c3lvwxq3grxw2zk5ilnijlan5yfhydmy2b4vjp7naf", "depends": ["AnnotationDbi", "GO_db", "biomaRt", "memoise"] }, "goSorensen": { "name": "goSorensen", "version": "1.10.0", "sha256": "0zrwhsqi2gjf1v3m5np1shnqfa8gj9kkzlpnpmdc0clarhxa1089", "depends": ["clusterProfiler", "goProfiles", "org_Hs_eg_db", "stringr"] }, "goTools": { "name": "goTools", "version": "1.82.0", "sha256": "0jcydnsjh9xacm3yazkjj493xyv54v6im9zp8kbk29a167fdd7qh", "depends": ["AnnotationDbi", "GO_db"] }, "goseq": { "name": "goseq", "version": "1.60.0", "sha256": "08ds2zaqkv7r9qcn8wnd994k94ifj848kg9q9swyq5gm8sg8sbn0", "depends": ["AnnotationDbi", "BiasedUrn", "BiocGenerics", "GO_db", "GenomeInfoDb", "GenomicFeatures", "geneLenDataBase", "mgcv", "rtracklayer"] }, "gpls": { "name": "gpls", "version": "1.80.0", "sha256": "1nzjm4h7xm9hvz62nmi57agwprrbdk8z4nfg4z0vx85cjrrz1k9h", "depends": [] }, "gpuMagic": { "name": "gpuMagic", "version": "1.23.0", "sha256": "0skgw46i3419i1bsinhkl12f1jv5gf2bxjr7j7ml5g7azypq61ha", "depends": ["BiocGenerics", "Deriv", "DescTools", "Rcpp", "digest", "pryr", "stringr"] }, "granulator": { "name": "granulator", "version": "1.16.0", "sha256": "0ycwj878nyf8vc131781abvpz5dmyhdprflidw6gz5ywz16l7538", "depends": ["MASS", "cowplot", "dplyr", "dtangle", "e1071", "epiR", "ggplot2", "ggplotify", "limSolve", "magrittr", "nnls", "pheatmap", "purrr", "rlang", "tibble", "tidyr"] }, "graper": { "name": "graper", "version": "1.24.2", "sha256": "067ppcg89dpi10qkqcnyyd7b3r15jwhmcczjzq2z2f8q4ahplp05", "depends": ["BH", "Matrix", "Rcpp", "RcppArmadillo", "cowplot", "ggplot2", "matrixStats"] }, "graph": { "name": "graph", "version": "1.86.0", "sha256": "0rzkz0nq4yzyr2165rw0grng3y21zyf36bgaa6l4hf5lzinik7mc", "depends": ["BiocGenerics"] }, "graphite": { "name": "graphite", "version": "1.54.0", "sha256": "0d0y8i2sswfkkdi0r9r28f4f41hp7qxxf5fxml39i5119bpkzzc5", "depends": ["AnnotationDbi", "graph", "httr", "purrr", "rappdirs", "rlang"] }, "groHMM": { "name": "groHMM", "version": "1.42.0", "sha256": "12b50lcsal9dmsgvfsccwa9w9h4askrfppfmfs9f99piyiavsvzz", "depends": ["GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "MASS", "S4Vectors", "rtracklayer"] }, "gscreend": { "name": "gscreend", "version": "1.22.0", "sha256": "0agcdswr2caislakgn5hk97p4jrmjp8k4ndfvhlhm3g42gpvxwca", "depends": ["BiocParallel", "SummarizedExperiment", "fGarch", "nloptr"] }, "gsean": { "name": "gsean", "version": "1.28.0", "sha256": "0hgk1jdp8qrjkh0x91d0d8l7jhsmmnhppn3jfr08gwwnjsmkkvr1", "depends": ["PPInfer", "fgsea"] }, "gtrellis": { "name": "gtrellis", "version": "1.40.0", "sha256": "1a0v1ks87rly0x8hw3x1qpkyjc4dadi6bnlrwfqkrx8m7nnzxjp9", "depends": ["GenomicRanges", "GetoptLong", "IRanges", "circlize"] }, "gwascat": { "name": "gwascat", "version": "2.40.0", "sha256": "048h1i0i6wm1rsnn6gcc83wf3bagwvbphqi7rbchkws8rn3828v9", "depends": ["AnnotationDbi", "AnnotationHub", "BiocFileCache", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "VariantAnnotation", "data_table", "readr", "snpStats", "tibble"] }, "gwasurvivr": { "name": "gwasurvivr", "version": "1.26.0", "sha256": "0m41pyq86v5x6bdpiq7rh395m34bcmp92c2pjcmr5vl885dg2qh8", "depends": ["GWASTools", "SNPRelate", "SummarizedExperiment", "VariantAnnotation", "matrixStats", "survival"] }, "gypsum": { "name": "gypsum", "version": "1.4.0", "sha256": "1mjlhn0026nfx4z7s4mdxd27b26vp5rklfqm2fksjizlid34h8fx", "depends": ["filelock", "httr2", "jsonlite", "rappdirs"] }, "h5mread": { "name": "h5mread", "version": "1.0.1", "sha256": "1dknsj8margcyh1ypdsc1qfn27d2m2ckch3phdlfj7nq7r4szfq5", "depends": ["BiocGenerics", "IRanges", "Rhdf5lib", "S4Arrays", "S4Vectors", "SparseArray", "rhdf5", "rhdf5filters"] }, "h5vc": { "name": "h5vc", "version": "2.42.0", "sha256": "19m73bmcv51v3kxa2i6khwpz39gfyf18ajnzikv91x1la9d347mw", "depends": ["BatchJobs", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rhtslib", "Rsamtools", "S4Vectors", "abind", "ggplot2", "gridExtra", "h5vcData", "reshape", "rhdf5"] }, "hapFabia": { "name": "hapFabia", "version": "1.50.0", "sha256": "1qg4128q340q3zfzlyby1kpbslnk6pqd34rzp3c3xn6d56dkq4zp", "depends": ["Biobase", "fabia"] }, "hca": { "name": "hca", "version": "1.16.0", "sha256": "1b2fj61m9h3h8ccly4y1ishr3ivrszpwc5j8rkkxy43nwmmv1r2p", "depends": ["BiocFileCache", "DT", "digest", "dplyr", "httr", "jsonlite", "miniUI", "readr", "shiny", "tibble", "tidyr"] }, "hdxmsqc": { "name": "hdxmsqc", "version": "1.4.0", "sha256": "0vhy1qfjh99c3z49r4smhxij49ji3arqlv77w4kbdp3ac4wfwisb", "depends": ["BiocStyle", "MsCoreUtils", "QFeatures", "S4Vectors", "Spectra", "dplyr", "ggplot2", "knitr", "tidyr"] }, "heatmaps": { "name": "heatmaps", "version": "1.32.0", "sha256": "0midacxd3k8hvvymgy8k3v5cm7b8hb3rph258agkkr3dyxlpb2dm", "depends": ["BiocGenerics", "Biostrings", "EBImage", "GenomeInfoDb", "GenomicRanges", "IRanges", "KernSmooth", "Matrix", "RColorBrewer", "plotrix"] }, "hermes": { "name": "hermes", "version": "1.12.1", "sha256": "0vlh3dg1a7kxgw6i3pcsn1xbs06b1s9i7hn946pm0fkcqappfx5n", "depends": ["Biobase", "BiocGenerics", "ComplexHeatmap", "DESeq2", "EnvStats", "GenomicRanges", "IRanges", "MultiAssayExperiment", "R6", "Rdpack", "S4Vectors", "SummarizedExperiment", "assertthat", "biomaRt", "checkmate", "circlize", "dplyr", "edgeR", "forcats", "ggfortify", "ggplot2", "ggrepel", "lifecycle", "limma", "magrittr", "matrixStats", "purrr", "rlang", "tidyr"] }, "hiAnnotator": { "name": "hiAnnotator", "version": "1.42.0", "sha256": "17c6v1w4lqiafvyfswf1p2wijzihawgazflwcviiq7dvx5qb0k6z", "depends": ["BSgenome", "GenomicRanges", "dplyr", "foreach", "ggplot2", "iterators", "rtracklayer", "scales"] }, "hiReadsProcessor": { "name": "hiReadsProcessor", "version": "1.44.0", "sha256": "0xql5p20cqhwb5j13l643lshhrns45n4hg15x8lbk24r2zmb8azi", "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "GenomicAlignments", "GenomicRanges", "dplyr", "hiAnnotator", "pwalign", "readxl", "sonicLength"] }, "hicVennDiagram": { "name": "hicVennDiagram", "version": "1.6.0", "sha256": "1ijzplniw4sm3bw62sfl7wr7ydbpdrq859iyxz9rsbxfmbkrclzd", "depends": ["ComplexUpset", "GenomeInfoDb", "GenomicRanges", "IRanges", "InteractionSet", "S4Vectors", "eulerr", "ggplot2", "htmlwidgets", "reshape2", "rtracklayer", "svglite"] }, "hierGWAS": { "name": "hierGWAS", "version": "1.38.0", "sha256": "0539jn026704hcn2zdi3srszf1wahsxb5ph79jl7m2hx8hns05zr", "depends": ["fastcluster", "fmsb", "glmnet"] }, "hierinf": { "name": "hierinf", "version": "1.26.0", "sha256": "10d5g0jcjidj4p4rajkg4f45nhgyqbwa6rlpbhwiljjk24lryjin", "depends": ["fmsb", "glmnet"] }, "hipathia": { "name": "hipathia", "version": "3.8.0", "sha256": "0lplbzcxgb1x5y5rqxr2jbl3a5fg7xh26p2i96mx39mmz8xvwnz0", "depends": ["AnnotationHub", "DelayedArray", "MetBrewer", "MultiAssayExperiment", "S4Vectors", "SummarizedExperiment", "coin", "dplyr", "ggplot2", "ggpubr", "igraph", "limma", "matrixStats", "preprocessCore", "reshape2", "servr", "tibble", "visNetwork"] }, "hmdbQuery": { "name": "hmdbQuery", "version": "1.28.0", "sha256": "0qd610p0cksa1l3vbmrfzxszvrpbc2b4q24537dq7cbkf7vrwdri", "depends": ["S4Vectors", "XML"] }, "hoodscanR": { "name": "hoodscanR", "version": "1.6.0", "sha256": "02xp81p1x8h2hykr3g70zm7ig86ljjz3rxsiy1p7j9xcp3fbkzjw", "depends": ["ComplexHeatmap", "RANN", "Rcpp", "SpatialExperiment", "SummarizedExperiment", "circlize", "ggplot2", "knitr", "rlang", "rmarkdown", "scico"] }, "hopach": { "name": "hopach", "version": "2.68.0", "sha256": "1p6cjcs0jws31v53kys3az4hlln92mr1wq711n71p2xmxj3bs69s", "depends": ["Biobase", "BiocGenerics", "cluster"] }, "hpar": { "name": "hpar", "version": "1.50.0", "sha256": "1r12x855l91jpcxllfink2dzw5gkpx5laq0krgn09rcbp87bm5zj", "depends": ["ExperimentHub"] }, "hummingbird": { "name": "hummingbird", "version": "1.18.0", "sha256": "0k9rvgfmgj33n2qzdz8b9mp1nxnsf9kk6k3qin5shiacdfa97ir3", "depends": ["GenomicRanges", "IRanges", "Rcpp", "SummarizedExperiment"] }, "hypeR": { "name": "hypeR", "version": "2.5.0", "sha256": "1c4ag9k8f91xyz3b57qrykj8kn467fh31lh41xw7vh1w7kwb0vjb", "depends": ["BiocStyle", "R6", "dplyr", "ggforce", "ggplot2", "htmltools", "httr", "igraph", "kableExtra", "magrittr", "msigdbr", "openxlsx", "purrr", "reactable", "reshape2", "rlang", "rmarkdown", "scales", "shiny", "stringr", "visNetwork"] }, "hyperdraw": { "name": "hyperdraw", "version": "1.60.0", "sha256": "1dq35dlcifqdkgh3nrry3h5rx3q948wvlw9g3kn3v7wy15lklh33", "depends": ["Rgraphviz", "graph", "hypergraph"] }, "hypergraph": { "name": "hypergraph", "version": "1.80.0", "sha256": "10a7c319ikn9yznf3b7m5vdwbycbjdjb0nc9b6wjvarw3775d77i", "depends": ["graph"] }, "iASeq": { "name": "iASeq", "version": "1.52.0", "sha256": "18xjfybwzqjgig2a7jhw2sbxq6f4893zj26dsfkzqljad3llvb02", "depends": [] }, "iBBiG": { "name": "iBBiG", "version": "1.52.0", "sha256": "10qg71bcw14wwla5vggb0q6m8cgmjvss792332qsvhhfvyxhz9ah", "depends": ["ade4", "biclust", "xtable"] }, "iBMQ": { "name": "iBMQ", "version": "1.48.0", "sha256": "0h916h1dgjmk4cd048rjccs76whm0p91byszfs6ynql4bzypdh0d", "depends": ["Biobase", "ggplot2"] }, "iCARE": { "name": "iCARE", "version": "1.36.0", "sha256": "17l8v8qi0mj7r6zcnv1zhhysk6p5bfviafxdjm3pdzb3cx9x6kiy", "depends": ["Hmisc", "gtools", "plotrix"] }, "iCNV": { "name": "iCNV", "version": "1.28.0", "sha256": "17gmfvpwm97ykpg2mwcp5ink8i6ry8bd0yi848xyb6q4s5i0yn7y", "depends": ["CODEX", "data_table", "dplyr", "fields", "ggplot2", "rlang", "tidyr", "truncnorm"] }, "iCOBRA": { "name": "iCOBRA", "version": "1.36.0", "sha256": "1dwrsjapgwh7q7q5qmy8k1iq5v5m2d3bz40jvnk7hqnm404qgzgf", "depends": ["DT", "ROCR", "UpSetR", "dplyr", "ggplot2", "limma", "markdown", "reshape2", "rlang", "scales", "shiny", "shinyBS", "shinydashboard"] }, "iCheck": { "name": "iCheck", "version": "1.38.0", "sha256": "1722j96py7fyaf5cla6alky0d0cmps5rb57wjgnhhvv1c0lvvpbs", "depends": ["Biobase", "GeneSelectMMD", "MASS", "affy", "gplots", "limma", "lmtest", "lumi", "preprocessCore", "randomForest", "rgl", "scatterplot3d"] }, "iChip": { "name": "iChip", "version": "1.62.0", "sha256": "0icv1nphpcznj18v5sk7yi3dhhk13x3q06yl87bwrswc6bzarqdf", "depends": ["limma"] }, "iClusterPlus": { "name": "iClusterPlus", "version": "1.44.0", "sha256": "150g1903yiwn2314pvwp8dnm1ba69ckbx6668p1yx8kdiz13kvwj", "depends": [] }, "iGC": { "name": "iGC", "version": "1.38.0", "sha256": "10qdwkqakhz7pjaqp1zla2mzg25gji99hx2mhhmpykq0999c0203", "depends": ["data_table", "plyr"] }, "iNETgrate": { "name": "iNETgrate", "version": "1.6.0", "sha256": "02862s4wqzmxhyvbk7d854wlp0whsww7g2w2ngwr5s4n1ri190p0", "depends": ["BiocStyle", "GenomicRanges", "Homo_sapiens", "Pigengene", "Rfast", "SummarizedExperiment", "WGCNA", "caret", "glmnet", "gplots", "igraph", "matrixStats", "minfi", "survival", "tidyr", "tidyselect"] }, "iPath": { "name": "iPath", "version": "1.14.0", "sha256": "0in8gcs669kcp397z5jishf26prgp86f7w86jwbdmi5j232xb9da", "depends": ["BiocParallel", "Rcpp", "RcppArmadillo", "ggplot2", "ggpubr", "matrixStats", "mclust", "survival", "survminer"] }, "iSEE": { "name": "iSEE", "version": "2.20.0", "sha256": "0vd6cgp6kz4nidic04drx335gy3ivf5j8sm8s3j6jm7qjl7pjwp4", "depends": ["BiocGenerics", "ComplexHeatmap", "DT", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "circlize", "colourpicker", "ggplot2", "ggrepel", "igraph", "listviewer", "mgcv", "rintrojs", "shiny", "shinyAce", "shinyWidgets", "shinydashboard", "shinyjs", "vipor", "viridisLite"] }, "iSEEde": { "name": "iSEEde", "version": "1.6.0", "sha256": "0hka6cq0jbxz8l7ymi85jwsqh9m8n1khwnngda8jx8w2y3snxgrl", "depends": ["DESeq2", "S4Vectors", "SummarizedExperiment", "edgeR", "iSEE", "shiny"] }, "iSEEfier": { "name": "iSEEfier", "version": "1.4.0", "sha256": "04gw4njrc3rb1c319s7qm26a42d5rww1pvy6h04cnah2vqa91j2y", "depends": ["BiocBaseUtils", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "iSEE", "iSEEu", "igraph", "rlang", "visNetwork"] }, "iSEEhex": { "name": "iSEEhex", "version": "1.10.0", "sha256": "16cl60f8h6qv31sry7plrh77636a38fsrx24rn3a57dyrrawyc10", "depends": ["SummarizedExperiment", "ggplot2", "hexbin", "iSEE", "shiny"] }, "iSEEhub": { "name": "iSEEhub", "version": "1.10.0", "sha256": "0rvviazpygr6qa5vqf1wfqgx07i0z9712j4zzmajmws1kc34gqk9", "depends": ["AnnotationHub", "BiocManager", "DT", "ExperimentHub", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "iSEE", "rintrojs", "shiny", "shinydashboard", "shinyjs"] }, "iSEEindex": { "name": "iSEEindex", "version": "1.6.0", "sha256": "0q1jdjxwnmg6jqgm6l5h25gk20yjg2lcvavaq9m9by7s9zwpc934", "depends": ["BiocFileCache", "DT", "SingleCellExperiment", "SummarizedExperiment", "iSEE", "paws_storage", "rintrojs", "shiny", "shinydashboard", "shinyjs", "stringr", "urltools"] }, "iSEEpathways": { "name": "iSEEpathways", "version": "1.6.0", "sha256": "1z150fbgx8z12ppnwr14g84mdrf133p7mavwvaynxs0lbfrjblzf", "depends": ["S4Vectors", "SummarizedExperiment", "ggplot2", "iSEE", "shiny", "shinyWidgets"] }, "iSEEtree": { "name": "iSEEtree", "version": "1.2.0", "sha256": "150zlmzdx1y19zjmwqnnw6qk97z57lq52d7s599lkc9va51x23r4", "depends": ["S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "TreeSummarizedExperiment", "ape", "ggplot2", "ggtree", "iSEE", "mia", "miaViz", "purrr", "shiny", "shinyWidgets", "tidygraph"] }, "iSEEu": { "name": "iSEEu", "version": "1.20.0", "sha256": "09g67nkb3g1lln2nsx80nym6rp19w58rb98k0kz679z74rip7k9x", "depends": ["DT", "IRanges", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "colourpicker", "ggplot2", "iSEE", "iSEEhex", "shiny", "shinyAce"] }, "iSeq": { "name": "iSeq", "version": "1.60.0", "sha256": "1bc2nplnayn0m32sya1dlrima9i54vhk6fc1s2lsfcng4xwxcv7d", "depends": [] }, "iasva": { "name": "iasva", "version": "1.26.0", "sha256": "0d9hp6dckilv5rcjijampzdlcbp7kg3pzx9d4x31wzrbl8154lw3", "depends": ["BiocParallel", "SummarizedExperiment", "cluster", "irlba"] }, "ibh": { "name": "ibh", "version": "1.56.0", "sha256": "028d3kj24cyipbyw5l7ahxpllmigxpz13s5dhg71rhf6gbinxpk8", "depends": ["simpIntLists"] }, "icetea": { "name": "icetea", "version": "1.26.0", "sha256": "0vdd65lw2c7ykqz4lica07k27iq21h7zgxkysjp4fbpysdplm2n1", "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "DESeq2", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "ShortRead", "SummarizedExperiment", "TxDb_Dmelanogaster_UCSC_dm6_ensGene", "VariantAnnotation", "csaw", "edgeR", "ggplot2", "limma", "rtracklayer"] }, "ideal": { "name": "ideal", "version": "2.2.0", "sha256": "1hgc14pnlfa10h0fjaz4yz6rhm509rw5mwm8icdlgdryxqpgvmh5", "depends": ["AnnotationDbi", "BiocParallel", "DESeq2", "DT", "GO_db", "GOstats", "GenomicRanges", "IHW", "IRanges", "S4Vectors", "SummarizedExperiment", "UpSetR", "base64enc", "dplyr", "ggplot2", "ggrepel", "goseq", "gplots", "heatmaply", "knitr", "limma", "mosdef", "pheatmap", "plotly", "rentrez", "rintrojs", "rlang", "rmarkdown", "shiny", "shinyAce", "shinyBS", "shinydashboard", "stringr", "topGO"] }, "idiogram": { "name": "idiogram", "version": "1.84.0", "sha256": "1zadfim9yrv3b0jqbfgr0vn86rnn3di0qx1d3w9gb54ghd4281l0", "depends": ["Biobase", "annotate", "plotrix"] }, "idpr": { "name": "idpr", "version": "1.18.0", "sha256": "1sl1vyhx5sbrylaz1h9xrsn95rhhizx9r0y0lk0vciz0i1n2wqv8", "depends": ["Biostrings", "dplyr", "ggplot2", "jsonlite", "magrittr", "plyr", "rlang"] }, "idr2d": { "name": "idr2d", "version": "1.22.0", "sha256": "0hj15k2525nnb440wsqksbv7wk1ghi9szf0n5dypvgd15lswgsaz", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "dplyr", "futile_logger", "ggplot2", "idr", "magrittr", "reticulate", "scales", "stringr"] }, "igvR": { "name": "igvR", "version": "1.28.0", "sha256": "0b6x3bmmanv046ddq2bxi0ggh79z983bsimpv6sfp6bzmnlm255s", "depends": ["BiocGenerics", "BrowserViz", "GenomicAlignments", "GenomicRanges", "RColorBrewer", "VariantAnnotation", "httpuv", "httr", "rtracklayer"] }, "igvShiny": { "name": "igvShiny", "version": "1.4.0", "sha256": "1rjz6jl5xm3s3l84q9izgrzmvwfg2irfhqc1l78dw4qnkmalqmk4", "depends": ["BiocGenerics", "GenomeInfoDbData", "GenomicRanges", "checkmate", "futile_logger", "htmlwidgets", "httr", "jsonlite", "randomcoloR", "shiny"] }, "illuminaio": { "name": "illuminaio", "version": "0.50.0", "sha256": "1azz7r90l9f7ns2p37qigwk45glq0p7rxkmgf939484iizkxq275", "depends": ["base64"] }, "imageTCGA": { "name": "imageTCGA", "version": "1.0.0", "sha256": "053q3wrqgq6j2wixjf23lysx9h4qbbww24856d9agjlgx5m6r20p", "depends": ["DT", "bsicons", "bslib", "clipr", "dplyr", "ggplot2", "leaflet", "rlang", "shiny", "tidyr", "viridis"] }, "imcRtools": { "name": "imcRtools", "version": "1.14.0", "sha256": "1118pdpi3fzkdl7k1q4q2m34r3hy7h72nsy48d4391ghdcf3hlmk", "depends": ["BiocNeighbors", "BiocParallel", "DT", "EBImage", "MatrixGenerics", "RTriangle", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "abind", "concaveman", "cytomapper", "data_table", "distances", "dplyr", "ggplot2", "ggraph", "igraph", "magrittr", "pheatmap", "readr", "rlang", "scuttle", "sf", "stringr", "tidygraph", "tidyselect", "viridis", "vroom"] }, "immApex": { "name": "immApex", "version": "1.2.5", "sha256": "1045g2ag0y84bcpcd26y58rrifx4q38gjy6gman9xlxnjxg0v221", "depends": ["SingleCellExperiment", "basilisk", "hash", "httr", "keras3", "magrittr", "matrixStats", "rvest", "stringi", "stringr", "tensorflow"] }, "immunoClust": { "name": "immunoClust", "version": "1.40.0", "sha256": "1m2caghphf47kv358psz11ydc7k9vapgcqqq60vhqpplclg51ry2", "depends": ["flowCore", "lattice"] }, "immunogenViewer": { "name": "immunogenViewer", "version": "1.1.1", "sha256": "1nvpv7m9r498mf21qmxina045qfn0ld2gwha8cscnjyx7m3a514y", "depends": ["UniProt_ws", "ggplot2", "httr", "jsonlite", "patchwork"] }, "immunotation": { "name": "immunotation", "version": "1.16.0", "sha256": "0ii5lhcwlr065kx7yjq3bby446i67msl4p3iyc9hxxbv4a8yqivf", "depends": ["curl", "ggplot2", "maps", "ontologyIndex", "readr", "rlang", "rvest", "stringr", "tidyr", "xml2"] }, "impute": { "name": "impute", "version": "1.82.0", "sha256": "1pmhz101nwab2f0p1afmb87b16rgd62ym724x4q30ll6rv5nc85s", "depends": [] }, "infercnv": { "name": "infercnv", "version": "1.24.0", "sha256": "0bix9cnb1bmbnjw5hfddl9hcg49j2gm9aaqr5sn2qf114by1pxr4", "depends": ["BiocGenerics", "HiddenMarkov", "Matrix", "RANN", "RColorBrewer", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "ape", "argparse", "caTools", "coda", "coin", "digest", "doParallel", "dplyr", "edgeR", "fastcluster", "fitdistrplus", "foreach", "futile_logger", "future", "ggplot2", "gplots", "gridExtra", "igraph", "parallelDist", "phyclust", "reshape2", "rjags", "tidyr"] }, "infinityFlow": { "name": "infinityFlow", "version": "1.18.0", "sha256": "03vx7k6q8w2amcv10y3d7a1cagzns8l1xk0a15hfqmyqygg8x700", "depends": ["Biobase", "flowCore", "generics", "gtools", "matlab", "pbapply", "png", "raster", "uwot", "xgboost"] }, "intansv": { "name": "intansv", "version": "1.48.0", "sha256": "14lcya7w4mp8i1c6ynhphakbf12ypqyyv7m1l6qmpy83dhd4djlk", "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "ggbio", "plyr"] }, "interacCircos": { "name": "interacCircos", "version": "1.18.0", "sha256": "0j7d2l7a4jr2qwfkw2jx4bvg0flwgv1yaw5p3kz32dnlsdxwlzdl", "depends": ["RColorBrewer", "htmlwidgets", "plyr"] }, "interactiveDisplay": { "name": "interactiveDisplay", "version": "1.46.0", "sha256": "0xx8rl1ifk631v39pmzi82zavi89m74p7pslgv2w40ms4fia9vgj", "depends": ["AnnotationDbi", "BiocGenerics", "Category", "RColorBrewer", "XML", "ggplot2", "gridSVG", "interactiveDisplayBase", "plyr", "reshape2", "shiny"] }, "interactiveDisplayBase": { "name": "interactiveDisplayBase", "version": "1.46.0", "sha256": "1xnllqanpfc8dghbzcd63dsycdagb1q8bvqpqv2isal9gpycw6q8", "depends": ["BiocGenerics", "DT", "shiny"] }, "ipdDb": { "name": "ipdDb", "version": "1.26.0", "sha256": "1djzg748zj8hl2z64lbs9kzrxbn65c817sz3zpl0xb5w1y20r4hg", "depends": ["AnnotationDbi", "AnnotationHub", "Biostrings", "DBI", "GenomicRanges", "IRanges", "RSQLite", "assertthat"] }, "islify": { "name": "islify", "version": "1.0.0", "sha256": "0439qhcn4xhcwcpbh4f6s3hf6xzv3yp8jrlymrgmdj3zklkic4mn", "depends": ["Matrix", "RBioFormats", "abind", "autothresholdr", "dbscan", "png", "tiff"] }, "isobar": { "name": "isobar", "version": "1.54.0", "sha256": "0z6qf3lngwlpzxv2mwlblwh640ixpsdiarq7wfhyxlzmjazw69vc", "depends": ["Biobase", "biomaRt", "distr", "ggplot2", "plyr"] }, "isomiRs": { "name": "isomiRs", "version": "1.36.1", "sha256": "1bcp2d2bc7fglq1kscxz8mdia6g8p80r3syvfrs42rql76hdvlfi", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "DEGreport", "DESeq2", "GGally", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "broom", "cluster", "cowplot", "dplyr", "ggplot2", "gplots", "gridExtra", "gtools", "limma", "readr", "reshape", "rlang", "stringr", "tibble", "tidyr"] }, "iterativeBMA": { "name": "iterativeBMA", "version": "1.66.0", "sha256": "0p449d50l8qi67hfzkqvb4cc3gx9l6vw2xqi9s4ymbikrj73rzyg", "depends": ["BMA", "Biobase", "leaps"] }, "iterativeBMAsurv": { "name": "iterativeBMAsurv", "version": "1.66.0", "sha256": "1lhmw5h19j0s5n5srpp1q1yl274rq682yx2nw63wvgwlnzl0xm57", "depends": ["BMA", "leaps", "survival"] }, "ivygapSE": { "name": "ivygapSE", "version": "1.30.0", "sha256": "078jm05dc6xmdhb9m3pqz8hr7fz5i0aqdyf2g8n3n3jjmhl45s9m", "depends": ["S4Vectors", "SummarizedExperiment", "UpSetR", "ggplot2", "hwriter", "plotly", "shiny", "survival", "survminer"] }, "jazzPanda": { "name": "jazzPanda", "version": "1.0.1", "sha256": "0l24f6w6kv7g08gjisqpl48cgd6zx5lzb14zi8j09l691gls1xgz", "depends": ["BiocParallel", "BumpyMatrix", "SpatialExperiment", "caret", "doParallel", "dplyr", "foreach", "glmnet", "magrittr", "spatstat_geom"] }, "karyoploteR": { "name": "karyoploteR", "version": "1.34.2", "sha256": "0n8cwyz0fv5k0m1pi4yqx2bph967029yb807jckyb90g2rldwwbp", "depends": ["AnnotationDbi", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "VariantAnnotation", "bamsignals", "bezier", "biovizBase", "digest", "memoise", "regioneR", "rtracklayer"] }, "katdetectr": { "name": "katdetectr", "version": "1.10.0", "sha256": "02dsxyxslqzyh57zf92wnlxlaw1nm9l7ykspkgbphsky4rchnd5q", "depends": ["BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "BSgenome_Hsapiens_UCSC_hg38", "Biobase", "BiocParallel", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rdpack", "S4Vectors", "VariantAnnotation", "changepoint", "changepoint_np", "checkmate", "dplyr", "ggplot2", "ggtext", "maftools", "plyranges", "rlang", "scales", "tibble", "tidyr"] }, "kebabs": { "name": "kebabs", "version": "1.42.0", "sha256": "1nzy5jbh545x9pc4vk7q0vraq9576yzg03wisavag8y7pn4k8k8f", "depends": ["Biostrings", "IRanges", "LiblineaR", "Matrix", "Rcpp", "S4Vectors", "XVector", "apcluster", "e1071", "kernlab"] }, "keggorthology": { "name": "keggorthology", "version": "2.60.0", "sha256": "01l9mii8liqnp0ghz1im5icwmw7i2q0228axjiz2ifnxffcf18iw", "depends": ["AnnotationDbi", "DBI", "graph", "hgu95av2_db"] }, "kissDE": { "name": "kissDE", "version": "1.28.0", "sha256": "1wkmkwib59hlgdvcfjq46igcnmrxyrz3zpmn93bpk40is0n0yxyk", "depends": ["Biobase", "DESeq2", "DSS", "DT", "ade4", "aods3", "doParallel", "factoextra", "foreach", "ggplot2", "gplots", "matrixStats", "shiny", "shinycssloaders"] }, "kmcut": { "name": "kmcut", "version": "1.2.0", "sha256": "18rbr8m5clgr1r2sw5kzbc31ikv9ibgckaygv1z3z50fi8klgv6i", "depends": ["S4Vectors", "SummarizedExperiment", "doParallel", "foreach", "pracma", "survival"] }, "knowYourCG": { "name": "knowYourCG", "version": "1.4.0", "sha256": "0pvkvgwqc137f1jym6cqasfiy3ppf4llx5fggsv8ff8p1hak2x64", "depends": ["GenomicRanges", "IRanges", "S4Vectors", "dplyr", "ggplot2", "ggrepel", "magrittr", "reshape2", "rlang", "sesameData", "stringr", "tibble", "wheatmap"] }, "koinar": { "name": "koinar", "version": "1.2.0", "sha256": "13jj9saqwrq7jcys973rcdiwk110b75jd4ijilhxhh4dhqc55kmr", "depends": ["httr", "jsonlite"] }, "ldblock": { "name": "ldblock", "version": "1.38.0", "sha256": "00yrl7yrwbx7f18g1y0kvyp9wqf95yqfx0ajm3karz123q5q3kpm", "depends": ["BiocGenerics", "Matrix", "httr", "rlang"] }, "lefser": { "name": "lefser", "version": "1.18.0", "sha256": "19hxbx3yqdg96mb857029qvj0whd1fa7g6abq35prkxf60pld5qh", "depends": ["BiocGenerics", "MASS", "S4Vectors", "SummarizedExperiment", "ape", "coin", "dplyr", "forcats", "ggplot2", "ggrepel", "ggtree", "mia", "purrr", "stringr", "testthat", "tibble", "tidyr", "tidyselect", "treeio"] }, "lemur": { "name": "lemur", "version": "1.6.1", "sha256": "1rhyh9r9mi3kybbfs0gvq0s7zb6qiy6d34qg44m6xkrj4ipwdhki", "depends": ["BiocGenerics", "BiocNeighbors", "DelayedMatrixStats", "HDF5Array", "Matrix", "MatrixGenerics", "Rcpp", "RcppArmadillo", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "glmGamPoi", "harmony", "irlba", "limma", "matrixStats", "rlang", "vctrs"] }, "les": { "name": "les", "version": "1.58.0", "sha256": "1gqxjgw1ffqqqzzaplriymlavx3v193p3inffh7bwchq4z02ksb1", "depends": ["RColorBrewer", "boot", "fdrtool", "gplots"] }, "levi": { "name": "levi", "version": "1.26.0", "sha256": "0awhv9zcy8jn0nxxcnk40w0yvjbg0xxhayvngqg89b7ja3jg1vfg", "depends": ["DT", "RColorBrewer", "Rcpp", "colorspace", "dplyr", "ggplot2", "httr", "igraph", "knitr", "reshape2", "rmarkdown", "shiny", "shinydashboard", "shinyjs", "testthat", "xml2"] }, "lfa": { "name": "lfa", "version": "2.8.0", "sha256": "00x7vjhsqfdbqf9lkx3lz93cqahdcdjawmfyvzyvdwjfxrmajfhb", "depends": ["RSpectra", "corpcor"] }, "limma": { "name": "limma", "version": "3.64.3", "sha256": "0vbm8cbnb9k1bx6bslib9lnm77fkf4zh07ixy1ybgbyspcq6liih", "depends": ["statmod"] }, "limmaGUI": { "name": "limmaGUI", "version": "1.84.0", "sha256": "1jixz7ilwg45aarzxf6zba169i947jdx3kabg0gb4ggzizjqrx22", "depends": ["R2HTML", "limma", "tkrplot", "xtable"] }, "limpa": { "name": "limpa", "version": "1.0.5", "sha256": "038qx6gniisgbjmiry7gidrg37vh2ddjsa4ydhv0843sjylpx6yw", "depends": ["data_table", "limma", "statmod"] }, "limpca": { "name": "limpca", "version": "1.4.0", "sha256": "0dv8ncklx9pmwx4z9kfaa7ivxi4cd2pbdprjf1a17jvg2a9x4qsk", "depends": ["S4Vectors", "SummarizedExperiment", "doParallel", "dplyr", "ggplot2", "ggrepel", "ggsci", "plyr", "reshape2", "stringr", "tibble", "tidyr", "tidyverse"] }, "lineagespot": { "name": "lineagespot", "version": "1.12.0", "sha256": "1n6x12ihigvz53av5gc1cw94fz45jiczawmvggykra1999k0f1yc", "depends": ["MatrixGenerics", "SummarizedExperiment", "VariantAnnotation", "data_table", "httr", "stringr"] }, "lionessR": { "name": "lionessR", "version": "1.22.0", "sha256": "1d0biddlzh237zwi72njf876rv0nhjmxfpyf9dfnvxcbz6hhiq0a", "depends": ["S4Vectors", "SummarizedExperiment"] }, "lipidr": { "name": "lipidr", "version": "2.22.1", "sha256": "0dy6jmlvgiz08xk7nniikhk49grrlli9p9cqqv36mvlq8rcg0v0n", "depends": ["S4Vectors", "SummarizedExperiment", "data_table", "dplyr", "fgsea", "forcats", "ggplot2", "imputeLCMD", "limma", "magrittr", "rlang", "ropls", "tidyr"] }, "lisaClust": { "name": "lisaClust", "version": "1.16.0", "sha256": "1pzdv5ivv75bhmjpsi3sagxc8w7zs9lsj5d5ildydsmifpfplab0", "depends": ["BiocGenerics", "BiocParallel", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "class", "concaveman", "data_table", "dplyr", "ggplot2", "lifecycle", "pheatmap", "purrr", "rlang", "simpleSeg", "spatstat_explore", "spatstat_geom", "spatstat_random", "spicyR", "tidyr"] }, "lmdme": { "name": "lmdme", "version": "1.50.0", "sha256": "1l1kwsp3lf5r3x7pwqa7j1s3f5w61zc3hxwpgbjkfd86vv6c129w", "depends": ["limma", "pls", "stemHypoxia"] }, "loci2path": { "name": "loci2path", "version": "1.28.0", "sha256": "1iwkwcxi593zyikjizs43li7f6r402m8a0m6n6b8a7f2nlblibzx", "depends": ["BiocParallel", "GenomicRanges", "RColorBrewer", "S4Vectors", "data_table", "pheatmap", "wordcloud"] }, "logicFS": { "name": "logicFS", "version": "2.28.0", "sha256": "1vps8qa10svfk5hxrj6xn9fmrbqn9mvph7rb1r419zr9z0p8nz4a", "depends": ["LogicReg", "mcbiopi", "survival"] }, "lpNet": { "name": "lpNet", "version": "2.40.0", "sha256": "02w8r6myyqbynynxmrzpjhxxdb8m04p9yxw7b4rmmi45052yamzd", "depends": ["KEGGgraph", "lpSolve"] }, "lpsymphony": { "name": "lpsymphony", "version": "1.36.0", "sha256": "1p1527hk52ca1qrsz0my887m01fq8zbnzs2z9hllpfgq633vissq", "depends": [] }, "lumi": { "name": "lumi", "version": "2.60.0", "sha256": "11j5jssdbip94njn2hbg2vk4wj2vn8vqnkr0i4dkd8vq1p40ps90", "depends": ["AnnotationDbi", "Biobase", "DBI", "GenomicFeatures", "GenomicRanges", "KernSmooth", "MASS", "RSQLite", "affy", "annotate", "lattice", "methylumi", "mgcv", "nleqslv", "preprocessCore"] }, "lute": { "name": "lute", "version": "1.4.0", "sha256": "1f1i083aqhls9xf7hynb1xlk5r9ksm5jzy9l971ikh97jyxfwx22", "depends": ["Biobase", "BiocGenerics", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "dplyr", "ggplot2", "scran"] }, "m6Aboost": { "name": "m6Aboost", "version": "1.14.0", "sha256": "1rdi20nwd4j1bqckhlyj8gc8pzrviwww7q3lh1h6hrc20lf8ckrz", "depends": ["BSgenome", "Biostrings", "ExperimentHub", "GenomicRanges", "IRanges", "S4Vectors", "adabag", "dplyr", "rtracklayer"] }, "mBPCR": { "name": "mBPCR", "version": "1.62.0", "sha256": "0swrs3x5yq6z63mwn0gzixacilb51nxzwgj9nnllhcl9kf8wmqxd", "depends": ["Biobase", "GWASTools", "oligoClasses"] }, "mCSEA": { "name": "mCSEA", "version": "1.28.0", "sha256": "0j1yrdl9im2s8xfzb57km43v2613k8h6hq29ypxqm6g4x95nhpqf", "depends": ["GenomicFeatures", "GenomicRanges", "Gviz", "Homo_sapiens", "IRanges", "S4Vectors", "SummarizedExperiment", "biomaRt", "fgsea", "ggplot2", "limma", "mCSEAdata"] }, "maCorrPlot": { "name": "maCorrPlot", "version": "1.78.0", "sha256": "1brq3mpa2wvzvp89cpwy8gr1b3yx63gq6avdavgkhpd2rfspyk2b", "depends": ["lattice"] }, "maPredictDSC": { "name": "maPredictDSC", "version": "1.46.0", "sha256": "0xygg4gfjs4ydq35855kailrcwm4w9fn9k9qm5fbncaybz79xzdw", "depends": ["AnnotationDbi", "LungCancerACvsSCCGEO", "MASS", "ROC", "ROCR", "affy", "caret", "class", "e1071", "gcrma", "hgu133plus2_db", "limma"] }, "maSigPro": { "name": "maSigPro", "version": "1.80.0", "sha256": "02vz1c9k3kgr8n7682sf040b693f46i75zxk4df5n31fvfwm91d7", "depends": ["Biobase", "MASS", "mclust", "venn"] }, "maaslin3": { "name": "maaslin3", "version": "1.0.0", "sha256": "14x7kblx19ibdclgj9qsy01w1d916xk88hhf7f4rqf2zl242vrck", "depends": ["BiocGenerics", "RColorBrewer", "SummarizedExperiment", "TreeSummarizedExperiment", "dplyr", "ggnewscale", "ggplot2", "lme4", "lmerTest", "logging", "multcomp", "optparse", "patchwork", "pbapply", "plyr", "rlang", "scales", "survival", "tibble"] }, "made4": { "name": "made4", "version": "1.82.0", "sha256": "0gzb8zw1npz04s5aihvnnch64ywgdfp1djxvy3a363kjl9wbiyrf", "depends": ["Biobase", "RColorBrewer", "SummarizedExperiment", "ade4", "gplots", "scatterplot3d"] }, "maftools": { "name": "maftools", "version": "2.24.0", "sha256": "16i7v706n1pi2p1n7jsd3wvx7j429f2n9gyfy2f2xxpm9h9bzvl7", "depends": ["DNAcopy", "RColorBrewer", "Rhtslib", "data_table", "pheatmap", "survival", "zlibbioc"] }, "magpie": { "name": "magpie", "version": "1.8.0", "sha256": "0rswjhicyn0yvc9pifyslpbxgqb2c5nv3kmzzs4crsygri2g16ax", "depends": ["AnnotationDbi", "BiocParallel", "DESeq2", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "RColorBrewer", "Rsamtools", "S4Vectors", "TRESS", "aod", "matrixStats", "openxlsx", "reshape2", "rtracklayer"] }, "magrene": { "name": "magrene", "version": "1.10.0", "sha256": "11b535p06ivk2c40nq42q7jrfrpbv2x7qlyjybvd7fh9zfy9r7kp", "depends": ["BiocParallel"] }, "makecdfenv": { "name": "makecdfenv", "version": "1.84.0", "sha256": "1wjlqh7q46slgnpzvij6gajgkcp4acqs146z365l22ywkm7b90q5", "depends": ["Biobase", "affy", "affyio"] }, "mapscape": { "name": "mapscape", "version": "1.32.0", "sha256": "0qzhc56hn4231kqf7l4m7drzbvw15hmmskn9fzgcbx81ak1qba35", "depends": ["base64enc", "htmlwidgets", "jsonlite", "stringr"] }, "mariner": { "name": "mariner", "version": "1.8.1", "sha256": "0m493hwhh03py8gbjqb520saz5qcwn80gl2j6xkw2yk4j33a16r8", "depends": ["BiocGenerics", "BiocManager", "BiocParallel", "DelayedArray", "GenomeInfoDb", "GenomicRanges", "HDF5Array", "IRanges", "InteractionSet", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "abind", "assertthat", "colourvalues", "data_table", "dbscan", "glue", "magrittr", "plotgardener", "plyranges", "progress", "purrr", "rhdf5", "rlang", "strawr"] }, "marr": { "name": "marr", "version": "1.18.0", "sha256": "1c21kssvg1ifs0ycsspssg38q3grl3ci2n676h0qb7hgx4138xqb", "depends": ["Rcpp", "S4Vectors", "SummarizedExperiment", "dplyr", "ggplot2", "magrittr", "rlang"] }, "marray": { "name": "marray", "version": "1.86.0", "sha256": "1ryj4rhikgc3997yasmll5zbbyh7x7qdfigyjadg18zsmghqbnjx", "depends": ["limma"] }, "martini": { "name": "martini", "version": "1.28.0", "sha256": "1wvlicmf472imy32v4r6jjwaw8g1ggpcppjb1i2fwgfxp249b7a4", "depends": ["Matrix", "Rcpp", "RcppEigen", "igraph", "memoise", "snpStats"] }, "maser": { "name": "maser", "version": "1.26.0", "sha256": "1qfiyjgjixw5iv077nk1c6biwwxj7jfykqvvn295gf69qahsvy4g", "depends": ["BiocGenerics", "DT", "GenomeInfoDb", "GenomicRanges", "Gviz", "IRanges", "data_table", "dplyr", "ggplot2", "reshape2", "rtracklayer"] }, "maskBAD": { "name": "maskBAD", "version": "1.52.0", "sha256": "1lw7r5r5z6qbj9j88wfyixy652a8wh10lkkcjx62039zsmdqgs8m", "depends": ["affy", "gcrma"] }, "massiR": { "name": "massiR", "version": "1.44.0", "sha256": "0fq97ig43432yfk40sa734jxdmd0birriffjrjbh9xqrhyg03m1j", "depends": ["Biobase", "cluster", "diptest", "gplots"] }, "mastR": { "name": "mastR", "version": "1.8.0", "sha256": "16zcqcbn3s7jrff5mlr3p07k0ngg6whcpijk849nn483sflzsr45", "depends": ["AnnotationDbi", "Biobase", "GSEABase", "Matrix", "SeuratObject", "SingleCellExperiment", "SummarizedExperiment", "dplyr", "edgeR", "ggplot2", "ggpubr", "limma", "msigdb", "org_Hs_eg_db", "patchwork", "tidyr"] }, "matchBox": { "name": "matchBox", "version": "1.50.0", "sha256": "0pyv16ymi5zj2hrlva8jdif42v1zkhn411k401mvqhscvpjs4z8q", "depends": [] }, "matter": { "name": "matter", "version": "2.10.0", "sha256": "0wb3iq390by21dgxy8ca9bh3schdfmf04800rn860lkiimivh2xj", "depends": ["BH", "BiocGenerics", "BiocParallel", "Matrix", "ProtGenerics", "digest", "irlba"] }, "mbQTL": { "name": "mbQTL", "version": "1.8.0", "sha256": "03pkbw1xwvf7cdvghaly08vdgyql78qyf6fsmhn6dl082ab09fx2", "depends": ["MatrixEQTL", "broom", "dplyr", "ggplot2", "metagenomeSeq", "pheatmap", "readxl", "stringr", "tidyr"] }, "mbkmeans": { "name": "mbkmeans", "version": "1.24.0", "sha256": "0ipb03c0k5w1y4bdm9fcpg1qih74phwwwmfqldabshbwhkkaw4rp", "depends": ["BiocParallel", "ClusterR", "DelayedArray", "Matrix", "Rcpp", "RcppArmadillo", "Rhdf5lib", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "beachmat", "benchmarkme"] }, "mdp": { "name": "mdp", "version": "1.28.0", "sha256": "1yy6g5xvm15r7h7p4yz30sf0a86kyy2xhfkcdhpdis0qhpsfvdx1", "depends": ["ggplot2", "gridExtra"] }, "mdqc": { "name": "mdqc", "version": "1.70.0", "sha256": "0x25jq8380rqgq04d1rjnvs5lb91gizwzfnj1i08gqiwb2b2ma6d", "depends": ["MASS", "cluster"] }, "megadepth": { "name": "megadepth", "version": "1.18.0", "sha256": "05b3vish9vx1a1pwqayc52hdqb5kimnpzn1kg8qv5979xjbs9s75", "depends": ["GenomicRanges", "cmdfun", "dplyr", "fs", "magrittr", "readr", "xfun"] }, "memes": { "name": "memes", "version": "1.16.0", "sha256": "1ivvnrnlz9239m2mvx804q1jli3rqzkagvhkjfi5m14v8rbb1zrc", "depends": ["Biostrings", "GenomicRanges", "cmdfun", "dplyr", "ggplot2", "ggseqlogo", "magrittr", "matrixStats", "patchwork", "processx", "purrr", "readr", "rlang", "tibble", "tidyr", "universalmotif", "usethis", "xml2"] }, "meshes": { "name": "meshes", "version": "1.34.0", "sha256": "1alqbcwi0ig5jfji1hi6m291y0ifm22j87nlkh2csb99fcs1j24f", "depends": ["AnnotationDbi", "AnnotationHub", "DOSE", "GOSemSim", "MeSHDbi", "enrichplot", "yulab_utils"] }, "meshr": { "name": "meshr", "version": "2.14.0", "sha256": "0cnmzz3ap6173410qa1qcy7xbcdr8ajzmdi6iykq0ahzyfdbnz6d", "depends": ["BiocGenerics", "BiocStyle", "Category", "MeSHDbi", "RSQLite", "S4Vectors", "fdrtool", "knitr", "markdown", "rmarkdown"] }, "messina": { "name": "messina", "version": "1.44.0", "sha256": "0kgdya5miyrylwh743m4d0vb1x984wa8bw53vqws0xf768fsn2fk", "depends": ["Rcpp", "foreach", "ggplot2", "plyr", "survival"] }, "metaCCA": { "name": "metaCCA", "version": "1.36.0", "sha256": "0x5lx3dwq50z1qx9njdirvxz6aiis9n0agdnzb2z9c2yc8c0vzdz", "depends": [] }, "metaMS": { "name": "metaMS", "version": "1.44.0", "sha256": "1xlss98wk95khfld03jf9abljj80q1mys856y6gz63xr6759szsv", "depends": ["BiocGenerics", "CAMERA", "Matrix", "robustbase", "xcms"] }, "metaSeq": { "name": "metaSeq", "version": "1.48.0", "sha256": "0svwvswj16nj2kswdgskwwam9w7vdkljn2hyyjawqwg0982llfim", "depends": ["NOISeq", "Rcpp", "snow"] }, "metabCombiner": { "name": "metabCombiner", "version": "1.18.0", "sha256": "0c2sspf2hq1malpz1yvqzb7i99bplixlmb4ymj8y6msycqdjldzp", "depends": ["S4Vectors", "caret", "dplyr", "matrixStats", "mgcv", "rlang", "tidyr"] }, "metabinR": { "name": "metabinR", "version": "1.10.0", "sha256": "072fb1rrr5bjl543y6ivb6rkw8f61wpw5cxv3cq07hghmik2k0q1", "depends": ["rJava"] }, "metabolomicsWorkbenchR": { "name": "metabolomicsWorkbenchR", "version": "1.18.0", "sha256": "1yk4ddcwqi72aq1jr7gj9c862g6fy82i0s7rx8a6y8nfigd1nvqd", "depends": ["MultiAssayExperiment", "SummarizedExperiment", "data_table", "httr", "jsonlite", "struct"] }, "metabomxtr": { "name": "metabomxtr", "version": "1.42.0", "sha256": "0h3yyq5f96z0qdmd16ard00sznyqiiv5nzz08x83y2br9vapfnx0", "depends": ["Biobase", "BiocParallel", "Formula", "ggplot2", "multtest", "optimx", "plyr"] }, "metagene2": { "name": "metagene2", "version": "1.24.0", "sha256": "00xnp9h2avmr5x8njangxgf1qa09rllxqlbnzs3vmcagl9d58yih", "depends": ["BiocParallel", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "R6", "Rsamtools", "data_table", "dplyr", "ggplot2", "magrittr", "purrr", "reshape2", "rtracklayer"] }, "metagenomeSeq": { "name": "metagenomeSeq", "version": "1.50.0", "sha256": "1xbyc6pd7q6pr6f86x0i5i3pfgd2i8z62zb4h1mpb3ypr12icacj", "depends": ["Biobase", "Matrix", "RColorBrewer", "Wrench", "foreach", "glmnet", "gplots", "limma", "matrixStats"] }, "metahdep": { "name": "metahdep", "version": "1.66.0", "sha256": "051jjcyww8m5dfk4ssvr2fvf9mym2nfsw27vmbz0cwd64kfv35cn", "depends": [] }, "metapod": { "name": "metapod", "version": "1.16.0", "sha256": "1hw8inkl6cxyf36cynwhcp1qxb8ls9w54gwwjf9ibsqpqw7in0ay", "depends": ["Rcpp"] }, "metapone": { "name": "metapone", "version": "1.14.0", "sha256": "1dc91jw9mw08wpa2flnprxn6vnv0rwc4wbfm6wr9fws5gwyxdnhv", "depends": ["BiocParallel", "fdrtool", "fgsea", "fields", "ggplot2", "ggrepel", "markdown"] }, "metaseqR2": { "name": "metaseqR2", "version": "1.20.0", "sha256": "16c0ic6mc48b7m2l96gy6m7qqfdpyp1nps82597zwbg6f3s53y2m", "depends": ["ABSSeq", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "DESeq2", "DSS", "DT", "EDASeq", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "MASS", "Matrix", "NBPSeq", "RSQLite", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VennDiagram", "biomaRt", "corrplot", "edgeR", "genefilter", "gplots", "harmonicmeanp", "heatmaply", "htmltools", "httr", "jsonlite", "lattice", "limma", "locfit", "log4r", "magrittr", "pander", "qvalue", "rmarkdown", "rmdformats", "rtracklayer", "stringr", "survcomp", "txdbmaker", "vsn", "yaml", "zoo"] }, "methInheritSim": { "name": "methInheritSim", "version": "1.30.0", "sha256": "1idnf3qwsymqhxn1sqjjmjf0w6fps519vla72r3493amipz8sb1l", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "methylKit", "msm"] }, "methimpute": { "name": "methimpute", "version": "1.30.0", "sha256": "04xidhw65jylc5gya5s2yjmbi5af2akvnsphpms0j5pnaiissfnm", "depends": ["Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rcpp", "data_table", "ggplot2", "minpack_lm", "reshape2"] }, "methodical": { "name": "methodical", "version": "1.4.0", "sha256": "0ybnr5pbmlrpsk19yz04c1iais6mklcq7xcrbs0c9wc5r0yxmidp", "depends": ["AnnotationHub", "BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "BSgenome_Hsapiens_UCSC_hg38", "BiocCheck", "BiocManager", "BiocParallel", "BiocStyle", "Biostrings", "DelayedArray", "ExperimentHub", "GenomeInfoDb", "GenomicRanges", "HDF5Array", "IRanges", "MatrixGenerics", "R_utils", "RcppRoll", "S4Vectors", "SummarizedExperiment", "TumourMethData", "annotatr", "cowplot", "data_table", "devtools", "dplyr", "foreach", "ggplot2", "knitr", "rcmdcheck", "remotes", "rhdf5", "rtracklayer", "scales", "tibble", "tidyr", "usethis"] }, "methrix": { "name": "methrix", "version": "1.22.1", "sha256": "0bw86bizpc12ffc9mhpg77wwcvw970jv2xmy9mln5zfhsgxq9zgg", "depends": ["BSgenome", "DelayedArray", "DelayedMatrixStats", "GenomicRanges", "HDF5Array", "IRanges", "S4Vectors", "SummarizedExperiment", "data_table", "ggplot2", "matrixStats", "rtracklayer"] }, "methyLImp2": { "name": "methyLImp2", "version": "1.4.0", "sha256": "1aaqrckxfpp9vfhj7fi19y924xrn8bcr24gpignkjfv4czxv89fh", "depends": ["BiocParallel", "ChAMPdata", "SummarizedExperiment", "corpcor"] }, "methylCC": { "name": "methylCC", "version": "1.22.0", "sha256": "0s8f1yj1qd648cxd3wxzjzbv0z7csrxsdhy6g3p5shn8piplqxk5", "depends": ["Biobase", "FlowSorted_Blood_450k", "GenomicRanges", "IRanges", "IlluminaHumanMethylation450kanno_ilmn12_hg19", "IlluminaHumanMethylation450kmanifest", "S4Vectors", "bsseq", "bumphunter", "dplyr", "genefilter", "magrittr", "minfi", "plyranges", "quadprog"] }, "methylGSA": { "name": "methylGSA", "version": "1.26.0", "sha256": "0bpas0zl4rf4gfvcp38y3v2cnlpc2a4n39ani1f7k91s5lvylkxx", "depends": ["AnnotationDbi", "BiocParallel", "GO_db", "IlluminaHumanMethylation450kanno_ilmn12_hg19", "IlluminaHumanMethylationEPICanno_ilm10b4_hg19", "RobustRankAggreg", "clusterProfiler", "ggplot2", "missMethyl", "org_Hs_eg_db", "reactome_db", "shiny", "stringr"] }, "methylInheritance": { "name": "methylInheritance", "version": "1.32.0", "sha256": "0dpq5vgb4zrj2pcwi0m8ykjvn0xr7hr4r0raksn8bgh0qyhn7mnf", "depends": ["BiocParallel", "GenomicRanges", "IRanges", "S4Vectors", "ggplot2", "gridExtra", "methylKit", "rebus"] }, "methylKit": { "name": "methylKit", "version": "1.34.0", "sha256": "09dc8h2w6xjkphfd82368lv9iq3yr46iiz05ixjjvlzvn772wqwd", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "KernSmooth", "R_utils", "Rcpp", "Rhtslib", "Rsamtools", "S4Vectors", "data_table", "emdbook", "fastseg", "gtools", "limma", "mclust", "mgcv", "qvalue", "rtracklayer"] }, "methylMnM": { "name": "methylMnM", "version": "1.46.0", "sha256": "1cls27s2qv18gggm1awz75ranng21w8rabs8cwj6spb11z5d5kzz", "depends": ["edgeR", "statmod"] }, "methylPipe": { "name": "methylPipe", "version": "1.42.1", "sha256": "1kv46iwy373l4dsnk7pa90cxz9dvs4xidhcxsnyw4zdd7flv8887", "depends": ["BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "Gviz", "IRanges", "Rsamtools", "S4Vectors", "SummarizedExperiment", "data_table", "gplots", "marray"] }, "methylSig": { "name": "methylSig", "version": "1.20.0", "sha256": "1ndsffrslk2m96f17mqpckd9igl3zva6r4xarxk89i3gl52y0xz1", "depends": ["DSS", "DelayedArray", "DelayedMatrixStats", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "bsseq"] }, "methylclock": { "name": "methylclock", "version": "1.14.0", "sha256": "1cyibj79zy3syqr2icqiddxphs1f4j24qihc8q96akj5ip7pisv6", "depends": ["Biobase", "ExperimentHub", "PerformanceAnalytics", "RPMM", "Rcpp", "devtools", "dplyr", "dynamicTreeCut", "ggplot2", "ggpmisc", "ggpubr", "gridExtra", "impute", "methylclockData", "minfi", "planet", "preprocessCore", "quadprog", "tibble", "tidyr", "tidyverse"] }, "methylscaper": { "name": "methylscaper", "version": "1.16.0", "sha256": "03896whn173rrzc7y4bxn8mljnqw3m9b3nm63jl5yv32x7scpkmw", "depends": ["BiocParallel", "Biostrings", "Rfast", "SummarizedExperiment", "data_table", "pwalign", "seqinr", "seriation", "shiny", "shinyFiles", "shinyjs"] }, "methylumi": { "name": "methylumi", "version": "2.54.0", "sha256": "1vxmwbhqsqjqgscw13094nz9y4izmi1a78b3i8npjwnxn330l9jk", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "FDb_InfiniumMethylation_hg19", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "annotate", "genefilter", "ggplot2", "illuminaio", "lattice", "matrixStats", "minfi", "reshape2", "scales"] }, "mfa": { "name": "mfa", "version": "1.30.0", "sha256": "0zgwf9sxgn0xb103f94zkd96264fjb7cshbwmbardlz74wvrjd87", "depends": ["Biobase", "MCMCglmm", "MCMCpack", "Rcpp", "coda", "dplyr", "ggmcmc", "ggplot2", "magrittr", "tibble"] }, "mgsa": { "name": "mgsa", "version": "1.56.0", "sha256": "0i8pncx71v58db7dpyibjkq938h4d4vmixyiy2pl4bjl4b0g081y", "depends": ["gplots"] }, "miQC": { "name": "miQC", "version": "1.16.0", "sha256": "0jdks2ra8v8lf46akyb9cchwhq7l457z1da2zfkw4kmrhbjdv4zc", "depends": ["SingleCellExperiment", "flexmix", "ggplot2"] }, "miRBaseConverter": { "name": "miRBaseConverter", "version": "1.32.0", "sha256": "1hivi18pmmf3y6w89ha2030gyq746bl42xmma159n2dn57svbwv7", "depends": [] }, "miRLAB": { "name": "miRLAB", "version": "1.38.0", "sha256": "1nksyiixwb8331phw07jgwbcbqw1flix10gi1yqn24cdg2q7k5qp", "depends": ["Category", "GOstats", "Hmisc", "InvariantCausalPrediction", "RCurl", "SummarizedExperiment", "TCGAbiolinks", "ctc", "dplyr", "energy", "entropy", "glmnet", "gplots", "httr", "impute", "limma", "org_Hs_eg_db", "pcalg", "stringr"] }, "miRNAmeConverter": { "name": "miRNAmeConverter", "version": "1.36.0", "sha256": "0vl9g12gjf0zgw9vxl0hnrm4d16cmcb67dd0alzhrdhz015c50wa", "depends": ["AnnotationDbi", "DBI", "miRBaseVersions_db", "reshape2"] }, "miRNApath": { "name": "miRNApath", "version": "1.68.0", "sha256": "0w9j0dp295153cvbmpkhs5n7nw3g4f6wpwkyp0qqipqi8n24hmzb", "depends": [] }, "miRNAtap": { "name": "miRNAtap", "version": "1.42.0", "sha256": "1aj7cm1sxc1s3c8m17bzprg1nafr1b7rgqhc7kn696gi20w8gqcd", "depends": ["AnnotationDbi", "DBI", "RSQLite", "plyr", "sqldf", "stringr"] }, "miRSM": { "name": "miRSM", "version": "2.4.0", "sha256": "0vkb5f9nycaijbk3ydalxc5f26l92iaxw69qywg99br7wl1kjxdv", "depends": ["BiBitR", "BicARE", "Biobase", "DOSE", "GFA", "GSEABase", "MCL", "MatrixCorrelation", "NMF", "PMA", "Rcpp", "ReactomePA", "SOMbrero", "SummarizedExperiment", "WGCNA", "biclust", "clusterProfiler", "dbscan", "dynamicTreeCut", "energy", "fabia", "flashClust", "iBBiG", "igraph", "isa2", "mclust", "org_Hs_eg_db", "ppclust", "rqubic"] }, "miRcomp": { "name": "miRcomp", "version": "1.38.1", "sha256": "0haz9h44r4s7f2sbsrglicss91qchjjgp6s9z8qj50zngkm9jdk2", "depends": ["Biobase", "KernSmooth", "miRcompData"] }, "miRspongeR": { "name": "miRspongeR", "version": "2.12.0", "sha256": "1lxd782xrdvd68h13795142930nrvkcg3h1b06h1x39573gs34dr", "depends": ["DOSE", "MCL", "Rcpp", "ReactomePA", "SPONGE", "clusterProfiler", "corpcor", "doParallel", "foreach", "igraph", "org_Hs_eg_db", "survival"] }, "mia": { "name": "mia", "version": "1.16.1", "sha256": "1b2g3g1qwg4gcl6a77wzxmx2c1mcbvfyy1135xkd8nicdyslbq8n", "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "DECIPHER", "DelayedArray", "DelayedMatrixStats", "DirichletMultinomial", "IRanges", "MASS", "MatrixGenerics", "MultiAssayExperiment", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "TreeSummarizedExperiment", "ape", "bluster", "decontam", "dplyr", "rbiom", "rlang", "scater", "scuttle", "stringr", "tibble", "tidyr", "vegan"] }, "miaDash": { "name": "miaDash", "version": "1.0.0", "sha256": "07dsqnbh9kv3p5h0hbzsfmw4cqwf6m16i0i04iz1prqx3qczlzis", "depends": ["S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "TreeSummarizedExperiment", "ape", "biomformat", "htmltools", "iSEE", "iSEEtree", "mia", "rintrojs", "scater", "shiny", "shinydashboard", "shinyjs", "vegan"] }, "miaSim": { "name": "miaSim", "version": "1.14.0", "sha256": "02qnkrsjl0qs66w5jvzz4yiqxjbckwi6p5nijq37n2xdv5bcqk4g", "depends": ["MatrixGenerics", "S4Vectors", "SummarizedExperiment", "TreeSummarizedExperiment", "deSolve", "poweRlaw"] }, "miaViz": { "name": "miaViz", "version": "1.16.0", "sha256": "005ny26n9w6l7dh0da5112h8g8fnridbsnn23rsphc45dbx9bz1a", "depends": ["BiocGenerics", "BiocParallel", "DelayedArray", "DirichletMultinomial", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "TreeSummarizedExperiment", "ape", "dplyr", "ggnewscale", "ggplot2", "ggraph", "ggrepel", "ggtree", "mia", "rlang", "scales", "scater", "tibble", "tidygraph", "tidyr", "tidytext", "tidytree", "viridis"] }, "microRNA": { "name": "microRNA", "version": "1.66.0", "sha256": "14qc1xvldplxv1pxfaizd5hgvkzb6gybrvg54mfihp04c1laxhgf", "depends": ["Biostrings"] }, "microSTASIS": { "name": "microSTASIS", "version": "1.8.0", "sha256": "1ixmd0srjndx43zsl183qzc1r4mhvm6cm2h5yshvijj4lhhgmfli", "depends": ["BiocParallel", "TreeSummarizedExperiment", "ggplot2", "ggside", "rlang", "stringr"] }, "microbiome": { "name": "microbiome", "version": "1.30.0", "sha256": "0l8538jg7rg8bag169ffbvhmb132y5rhn6s7a906jd2kf5fyx6ja", "depends": ["Biostrings", "Rtsne", "compositions", "dplyr", "ggplot2", "phyloseq", "reshape2", "scales", "tibble", "tidyr", "vegan"] }, "microbiomeDASim": { "name": "microbiomeDASim", "version": "1.22.0", "sha256": "11lp6gdgvc6yg93ndxy50aya6apy6r5sxa13wx9p6bj9a0x7cnmg", "depends": ["Biobase", "MASS", "Matrix", "ggplot2", "metagenomeSeq", "mvtnorm", "pbapply", "phyloseq", "tmvtnorm"] }, "microbiomeExplorer": { "name": "microbiomeExplorer", "version": "1.18.0", "sha256": "195rmgpzjfr09anv2dbl5njnilylqlxl7q1isg42fvprqd4bf587", "depends": ["Biobase", "DESeq2", "DT", "RColorBrewer", "biomformat", "broom", "car", "dplyr", "forcats", "heatmaply", "knitr", "limma", "lubridate", "magrittr", "matrixStats", "metagenomeSeq", "plotly", "purrr", "readr", "reshape2", "rlang", "rmarkdown", "shiny", "shinyWidgets", "shinycssloaders", "shinydashboard", "shinyjs", "stringr", "tibble", "tidyr", "vegan"] }, "midasHLA": { "name": "midasHLA", "version": "1.16.0", "sha256": "1cpmd8g0lmd567aqkzb1nidqz1qabrlsywwpdwxya0bdd45a8wz0", "depends": ["HardyWeinberg", "MultiAssayExperiment", "S4Vectors", "SummarizedExperiment", "assertthat", "broom", "dplyr", "formattable", "kableExtra", "knitr", "magrittr", "qdapTools", "rlang", "stringi", "tibble"] }, "miloR": { "name": "miloR", "version": "2.4.1", "sha256": "0y8zdljfyd2hq8c90dcaljrycfmbjs0c3v59w5ynhzqnr3mx8wls", "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "Matrix", "MatrixGenerics", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RcppML", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "cowplot", "dplyr", "edgeR", "ggbeeswarm", "ggplot2", "ggraph", "ggrepel", "gtools", "igraph", "irlba", "limma", "matrixStats", "numDeriv", "patchwork", "pracma", "stringr", "tibble", "tidyr"] }, "mimager": { "name": "mimager", "version": "1.32.0", "sha256": "1yb3wgc5ghw4k1sg8a9p00ff7dg4lbbghvp0mszagy1q7kllh9i1", "depends": ["Biobase", "BiocGenerics", "DBI", "S4Vectors", "affy", "affyPLM", "gtable", "oligo", "oligoClasses", "preprocessCore", "scales"] }, "mina": { "name": "mina", "version": "1.16.0", "sha256": "1jbygw7gzqrirdkq3c0p5hz9hbmaybj5aqcd2pd75dcy6lnvyk0v", "depends": ["Hmisc", "MCL", "RSpectra", "Rcpp", "RcppArmadillo", "RcppParallel", "apcluster", "biganalytics", "bigmemory", "foreach", "ggplot2", "parallelDist", "plyr", "reshape2", "stringr"] }, "minet": { "name": "minet", "version": "3.66.0", "sha256": "1gbpi6nxla161zpmlpymvalchcgk4f97rz9kw49bnbr1lw8msa84", "depends": ["infotheo"] }, "minfi": { "name": "minfi", "version": "1.54.1", "sha256": "19sp391aqjlynwgmb8hk211dp5gcjwqv0m1407m4by9pgrg1x21r", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "DelayedArray", "DelayedMatrixStats", "GEOquery", "GenomeInfoDb", "GenomicRanges", "HDF5Array", "IRanges", "MASS", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "beanplot", "bumphunter", "data_table", "genefilter", "illuminaio", "lattice", "limma", "mclust", "nlme", "nor1mix", "preprocessCore", "quadprog", "reshape", "siggenes"] }, "mirIntegrator": { "name": "mirIntegrator", "version": "1.38.0", "sha256": "05d5x4xzqz2bpi7wvbf8nx5x6cn24hmc4acq04b7g7fs3mj0zd2v", "depends": ["AnnotationDbi", "ROntoTools", "Rgraphviz", "ggplot2", "graph", "org_Hs_eg_db"] }, "mirTarRnaSeq": { "name": "mirTarRnaSeq", "version": "1.16.0", "sha256": "0zlhkcip070xvmb58lqn61ajihcz8i7w2y5dpvxq0rm4hg5yhnbb", "depends": ["MASS", "R_utils", "assertthat", "caTools", "corrplot", "data_table", "dplyr", "ggplot2", "pheatmap", "pscl", "purrr", "reshape2", "viridis"] }, "missMethyl": { "name": "missMethyl", "version": "1.42.0", "sha256": "10sb3800dvic1nhan3g3gsmhqa4mbk22fwiyz08gq97bka4g3adp", "depends": ["AnnotationDbi", "BiasedUrn", "Biobase", "BiocGenerics", "GO_db", "GenomicRanges", "IRanges", "IlluminaHumanMethylation450kanno_ilmn12_hg19", "IlluminaHumanMethylation450kmanifest", "IlluminaHumanMethylationEPICanno_ilm10b4_hg19", "IlluminaHumanMethylationEPICmanifest", "IlluminaHumanMethylationEPICv2anno_20a1_hg38", "IlluminaHumanMethylationEPICv2manifest", "S4Vectors", "SummarizedExperiment", "limma", "methylumi", "minfi", "org_Hs_eg_db", "ruv", "statmod", "stringr"] }, "missRows": { "name": "missRows", "version": "1.28.0", "sha256": "0p979nxxwrzwn4pjxhy4hzrsa14j1y38sayinfzm6w04f9qhygdj", "depends": ["MultiAssayExperiment", "S4Vectors", "ggplot2", "gtools", "plyr"] }, "mist": { "name": "mist", "version": "1.0.0", "sha256": "1y1k3xz0di4g26hfplqv9cbnivmaws0wgxgz7qgyz2b27x13gkmw", "depends": ["BiocGenerics", "BiocParallel", "MCMCpack", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "car", "mvtnorm", "rlang", "rtracklayer"] }, "mistyR": { "name": "mistyR", "version": "1.16.0", "sha256": "0wndy978qly0m9nk5q3ilycrk50198zbczxwsg8c2pm12i120fj1", "depends": ["R_utils", "assertthat", "caret", "deldir", "digest", "distances", "dplyr", "filelock", "furrr", "ggplot2", "purrr", "ranger", "readr", "ridge", "rlang", "rlist", "stringr", "tibble", "tidyr", "tidyselect", "withr"] }, "mitch": { "name": "mitch", "version": "1.20.0", "sha256": "1s7mqb4qxx2ylr966y0aj3m9slvcrxy5zxj77q7nfi256781lf4x", "depends": ["GGally", "MASS", "beeswarm", "dplyr", "echarts4r", "ggplot2", "gplots", "gridExtra", "kableExtra", "knitr", "network", "plyr", "reshape2", "rmarkdown"] }, "mitoClone2": { "name": "mitoClone2", "version": "1.14.0", "sha256": "1p7mg1cb8ma161hbhjpa7xcigszmzjwvgqv12gpadmn080z8lljm", "depends": ["GenomicRanges", "Rhtslib", "S4Vectors", "deepSNV", "ggplot2", "pheatmap", "reshape2"] }, "mitology": { "name": "mitology", "version": "1.0.0", "sha256": "1kvka6ma0ax74521w31nijz0nkq9dl56f76ab1i9h6pr3jaaddj3", "depends": ["AnnotationDbi", "ComplexHeatmap", "ape", "circlize", "ggplot2", "ggtree", "magrittr", "org_Hs_eg_db", "scales"] }, "mixOmics": { "name": "mixOmics", "version": "6.32.0", "sha256": "177wpgpd5przj4zfj9ylwr1xxlq9a2yjp6kjkca9h79r4mgba1sn", "depends": ["BiocParallel", "MASS", "RColorBrewer", "corpcor", "dplyr", "ellipse", "ggplot2", "ggrepel", "gridExtra", "gsignal", "igraph", "lattice", "matrixStats", "rARPACK", "reshape2", "rgl", "tidyr"] }, "mnem": { "name": "mnem", "version": "1.24.0", "sha256": "077g7pmlx8qlj4hnn2xlyn1h0ydv0pxwjxc4jsmn7ni8hzcppi80", "depends": ["Linnorm", "Rcpp", "RcppEigen", "Rgraphviz", "cluster", "data_table", "e1071", "flexclust", "ggplot2", "graph", "lattice", "matrixStats", "naturalsort", "snowfall", "tsne", "wesanderson"] }, "moanin": { "name": "moanin", "version": "1.16.1", "sha256": "00361hb8ccnf01a7qx5qa8h4i1cicg71w40hi28mmr20q94rahxj", "depends": ["ClusterR", "MASS", "NMI", "S4Vectors", "SummarizedExperiment", "edgeR", "limma", "matrixStats", "reshape2", "topGO", "viridis", "zoo"] }, "mobileRNA": { "name": "mobileRNA", "version": "1.4.0", "sha256": "0a7kd7a2avkiba4aixyv8bvk7rha91g25hg16nbkikv5px1x7ssw", "depends": ["BiocGenerics", "Biostrings", "DESeq2", "GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "SimDesign", "SummarizedExperiment", "bioseq", "data_table", "dplyr", "edgeR", "ggplot2", "ggrepel", "pheatmap", "progress", "reticulate", "rlang", "rtracklayer", "scales", "tidyr", "tidyselect"] }, "mogsa": { "name": "mogsa", "version": "1.42.0", "sha256": "13zfxl0saqs57i29ymrpx46awjljihhhvkylj86hv35x4ly4hql5", "depends": ["Biobase", "BiocGenerics", "GSEABase", "cluster", "corpcor", "genefilter", "gplots", "graphite", "svd"] }, "monaLisa": { "name": "monaLisa", "version": "1.14.0", "sha256": "16rp6c0hcl0xmw08xpq649sdf5dgcn4s8394lq562rrbb51wvsg4", "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "ComplexHeatmap", "GenomeInfoDb", "GenomicRanges", "IRanges", "RSQLite", "S4Vectors", "SummarizedExperiment", "TFBSTools", "XVector", "circlize", "cli", "ggplot2", "glmnet", "rlang", "stabs", "tidyr"] }, "monocle": { "name": "monocle", "version": "2.36.0", "sha256": "0lp75gdxizsap5shsavdiq6c0vlkaw81qsd4k8sna90hr7bziwv3", "depends": ["Biobase", "BiocGenerics", "DDRTree", "HSMMSingleCell", "MASS", "Matrix", "RANN", "Rcpp", "Rtsne", "VGAM", "biocViews", "cluster", "combinat", "dplyr", "fastICA", "ggplot2", "igraph", "irlba", "leidenbase", "limma", "matrixStats", "pheatmap", "plyr", "proxy", "reshape2", "slam", "stringr", "tibble", "viridis"] }, "mosaics": { "name": "mosaics", "version": "2.46.0", "sha256": "1ya14fdxbbcflhiknmx8ar29y1sbpdih9q8g381s4vlli3k3zgxk", "depends": ["GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "MASS", "Rcpp", "Rsamtools", "S4Vectors", "lattice"] }, "mosbi": { "name": "mosbi", "version": "1.14.0", "sha256": "160yz2bqx7rm8m90j282yr3dkaw3r1ckhnikb6zw4xkd7nwj3wkl", "depends": ["BH", "QUBIC", "RColorBrewer", "Rcpp", "RcppParallel", "akmbiclust", "biclust", "fabia", "igraph", "isa2", "xml2"] }, "mosdef": { "name": "mosdef", "version": "1.4.1", "sha256": "1grj51fvandhmh9kgaiwf9mryim2snfrw1bbi8v214r14v86s9gz", "depends": ["AnnotationDbi", "DESeq2", "DT", "GO_db", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "clusterProfiler", "ggforce", "ggplot2", "ggrepel", "goseq", "htmltools", "rlang", "scales", "topGO"] }, "motifStack": { "name": "motifStack", "version": "1.52.0", "sha256": "1gd8rhdci6cskhxz6g5hyjx9rdpd5b6pacy5i8nk5yvqmg2jqwrn", "depends": ["Biostrings", "TFBSTools", "XML", "ade4", "ggplot2", "htmlwidgets"] }, "motifTestR": { "name": "motifTestR", "version": "1.4.0", "sha256": "0qdivy6ci9xcjjwbkklh69rqhfrvi733r2jraw9cina8jiwff2q9", "depends": ["Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "ggplot2", "harmonicmeanp", "matrixStats", "patchwork", "rlang", "universalmotif"] }, "motifbreakR": { "name": "motifbreakR", "version": "2.22.0", "sha256": "1kc9aqpx7006c5pz0i7l8qvp0vkng9f14r7z1wj67rb806qsd76f", "depends": ["BSgenome", "BiocFileCache", "BiocGenerics", "BiocParallel", "Biostrings", "DT", "GenomeInfoDb", "GenomicRanges", "Gviz", "IRanges", "MotifDb", "S4Vectors", "SummarizedExperiment", "TFMPvalue", "VariantAnnotation", "biomaRt", "bsicons", "bslib", "matrixStats", "motifStack", "pwalign", "rtracklayer", "shiny", "stringr", "vroom"] }, "motifcounter": { "name": "motifcounter", "version": "1.32.0", "sha256": "19wfy5cn76x9v7sb3pglk3c7lw997cidmsl39hhdyxsm76nfy0cv", "depends": ["Biostrings"] }, "motifmatchr": { "name": "motifmatchr", "version": "1.30.0", "sha256": "0j0dx8v856l4bqz0v3n2kj4yvdq4ffkfr5vsh5mwj09vbacjqzgf", "depends": ["BSgenome", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "Matrix", "Rcpp", "RcppArmadillo", "Rsamtools", "S4Vectors", "SummarizedExperiment", "TFBSTools"] }, "mpra": { "name": "mpra", "version": "1.30.1", "sha256": "1jdd51rjhzx8l3cj00l9z7bpxhqiiw47qhsv49av2qf5rf94w2bk", "depends": ["BiocGenerics", "S4Vectors", "SummarizedExperiment", "limma", "scales", "statmod"] }, "msImpute": { "name": "msImpute", "version": "1.18.0", "sha256": "1f05avwrxfbr4jf14x23w9zay74lnwfji82vbkjdsaxxsx3rwnw6", "depends": ["FNN", "data_table", "dplyr", "limma", "matrixStats", "mvtnorm", "pdist", "reticulate", "scran", "softImpute", "tidyr"] }, "msPurity": { "name": "msPurity", "version": "1.34.0", "sha256": "1q20wrlzb51ri3sz70zxw65gg538jqvrl42hmrk8d2h1yl6ipxvm", "depends": ["DBI", "RSQLite", "Rcpp", "dbplyr", "doSNOW", "dplyr", "fastcluster", "foreach", "ggplot2", "magrittr", "mzR", "plyr", "reshape2", "stringr"] }, "msa": { "name": "msa", "version": "1.40.0", "sha256": "0cfxdyynnzb06cv9mghsbpkrqi66yrcfy4crzfwlszdxf5ixdqyb", "depends": ["BiocGenerics", "Biostrings", "IRanges", "Rcpp", "S4Vectors"] }, "msgbsR": { "name": "msgbsR", "version": "1.32.0", "sha256": "1j77bc05slhgznwmg6lym9vzk61dvhjd2iisksz1yn635cflfryp", "depends": ["BSgenome", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "R_utils", "Rsamtools", "S4Vectors", "SummarizedExperiment", "easyRNASeq", "edgeR", "ggbio", "ggplot2", "plyr"] }, "mslp": { "name": "mslp", "version": "1.10.0", "sha256": "1za9q8hmia7d8f795v7v53n4vadpyk8irmsszna3va6kk0ir1fby", "depends": ["RankProd", "data_table", "doRNG", "fmsb", "foreach", "magrittr", "org_Hs_eg_db", "pROC", "randomForest"] }, "msmsEDA": { "name": "msmsEDA", "version": "1.46.0", "sha256": "1qxksn69zp1whxajwzdprpns9r1aq66hkgp9knc8nd2jk5y8arla", "depends": ["MASS", "MSnbase", "RColorBrewer", "gplots"] }, "msmsTests": { "name": "msmsTests", "version": "1.46.0", "sha256": "0vy90ki0fcyszry21m53yf1rpa59y80m9y1sjbhkcn0qxwplf593", "depends": ["MSnbase", "edgeR", "msmsEDA", "qvalue"] }, "mspms": { "name": "mspms", "version": "1.0.0", "sha256": "0bcjyw5d3l9f2h9157acxpjfn2shpgv4191p6880j77s5vi20xb5", "depends": ["QFeatures", "SummarizedExperiment", "dplyr", "ggplot2", "ggpubr", "ggseqlogo", "heatmaply", "limma", "magrittr", "purrr", "readr", "rlang", "rstatix", "stringr", "tibble", "tidyr"] }, "msqrob2": { "name": "msqrob2", "version": "1.16.0", "sha256": "0ik80pmwzyaaz287hab3nfivag4pzd1qkngc91vlmx21x0r4nzss", "depends": ["BiocParallel", "MASS", "Matrix", "MultiAssayExperiment", "QFeatures", "SummarizedExperiment", "codetools", "limma", "lme4", "purrr"] }, "multiClust": { "name": "multiClust", "version": "1.38.0", "sha256": "0hm1hpjaf5rnxzxlxpxhwsz3xdx2n1yvw5ljk7f2mslbphnbfmb6", "depends": ["amap", "cluster", "ctc", "dendextend", "mclust", "survival"] }, "multiGSEA": { "name": "multiGSEA", "version": "1.18.0", "sha256": "0mxl9lgwv9gxb671fynhkl3mj9d5j6df2j9yr2w1g7bgp80hw434", "depends": ["AnnotationDbi", "dplyr", "fgsea", "graphite", "magrittr", "metaboliteIDmapping", "metap", "rappdirs", "rlang"] }, "multiHiCcompare": { "name": "multiHiCcompare", "version": "1.26.0", "sha256": "00gw159yyas5b8122z096rgiyr215i9c35way67s73h2zl8jbrs7", "depends": ["BiocParallel", "GenomeInfoDb", "GenomeInfoDbData", "GenomicRanges", "HiCcompare", "aggregation", "data_table", "dplyr", "edgeR", "pbapply", "pheatmap", "qqman"] }, "multiMiR": { "name": "multiMiR", "version": "1.30.0", "sha256": "0f64qmiv6kq6md4clyk369pp8zyzyygxw8wllrwmyik8y9zqfsxz", "depends": ["AnnotationDbi", "BiocGenerics", "RCurl", "XML", "dplyr", "purrr", "tibble"] }, "multiWGCNA": { "name": "multiWGCNA", "version": "1.6.0", "sha256": "0p14v9kdg105jlglcm24h0mvrn7f4x7r4k1la3l5wlyk17jga24q", "depends": ["SummarizedExperiment", "WGCNA", "cowplot", "data_table", "dcanr", "dplyr", "flashClust", "ggalluvial", "ggplot2", "ggrepel", "igraph", "patchwork", "readr", "reshape2", "scales", "stringr"] }, "multicrispr": { "name": "multicrispr", "version": "1.18.0", "sha256": "1q6s3rr6w66gykfh304sk3mw6ja8hxpszikvjyxjz1liyzqmarwr", "depends": ["BSgenome", "BiocGenerics", "Biostrings", "CRISPRseek", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "Rbowtie", "data_table", "ggplot2", "karyoploteR", "magrittr", "plyranges", "reticulate", "rtracklayer", "stringi", "tidyr", "tidyselect"] }, "multiscan": { "name": "multiscan", "version": "1.68.0", "sha256": "0zq5gd4x28ilh70bdd535w2sgdssw6ddgnljah74fbjmxjj9q2p2", "depends": ["Biobase"] }, "multistateQTL": { "name": "multistateQTL", "version": "2.0.0", "sha256": "1b4is7chha5w4ivvk5w5rpl7033bb0r8m72baz553dzrhzp8imvc", "depends": ["ComplexHeatmap", "QTLExperiment", "S4Vectors", "SummarizedExperiment", "circlize", "collapse", "data_table", "dplyr", "fitdistrplus", "ggplot2", "mashr", "matrixStats", "tidyr", "viridis"] }, "multtest": { "name": "multtest", "version": "2.64.0", "sha256": "0fcqz532n7p2ip2awm9if4yn39z0mgwcjl7p0gyhp79nlv6fcdmr", "depends": ["Biobase", "BiocGenerics", "MASS", "survival"] }, "mumosa": { "name": "mumosa", "version": "1.16.0", "sha256": "0scdf663lwpz1hzcz5kbh28x4vvkqrdvhhwf523l3h7mlyqrwgqx", "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "DelayedArray", "DelayedMatrixStats", "IRanges", "Matrix", "S4Vectors", "ScaledMatrix", "SingleCellExperiment", "SummarizedExperiment", "batchelor", "beachmat", "igraph", "metapod", "scran", "scuttle", "uwot"] }, "muscat": { "name": "muscat", "version": "1.22.0", "sha256": "1gbh93xb82k16wjwavpf8bfzb5fy5i4rpq5a174cjzi9idndjsra", "depends": ["BiocParallel", "ComplexHeatmap", "DESeq2", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "blme", "data_table", "dplyr", "edgeR", "ggplot2", "glmmTMB", "limma", "lme4", "lmerTest", "matrixStats", "progress", "purrr", "rlang", "scales", "scater", "sctransform", "scuttle", "variancePartition", "viridis"] }, "muscle": { "name": "muscle", "version": "3.50.0", "sha256": "03inf7jdmm03rgliwr4y80zpmbkl5aki6z475ayr8b2dbqvpy4f2", "depends": ["Biostrings"] }, "musicatk": { "name": "musicatk", "version": "2.2.1", "sha256": "115zg1ypa4jks26zg7rwg8a3pk1nh43c3760dfbk89szyry4vxq9", "depends": ["BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "BSgenome_Hsapiens_UCSC_hg38", "BSgenome_Mmusculus_UCSC_mm10", "BSgenome_Mmusculus_UCSC_mm9", "Biostrings", "ComplexHeatmap", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "MASS", "MCMCprecision", "Matrix", "NMF", "S4Vectors", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "VariantAnnotation", "cluster", "data_table", "decompTumor2Sig", "dplyr", "factoextra", "ggplot2", "ggpubr", "ggrepel", "gridExtra", "gtools", "maftools", "magrittr", "matrixTests", "philentropy", "plotly", "rlang", "scales", "shiny", "stringi", "stringr", "tibble", "tidyr", "tidyverse", "topicmodels", "uwot"] }, "mygene": { "name": "mygene", "version": "1.44.0", "sha256": "18wk3ks222pwamq62pyfjwwrpkkj842p79wsnjbvx6km0fqycr16", "depends": ["GenomicFeatures", "Hmisc", "S4Vectors", "httr", "jsonlite", "plyr", "sqldf", "txdbmaker"] }, "myvariant": { "name": "myvariant", "version": "1.38.0", "sha256": "1kl4cndr9a5ri7zxl274z6d6a7584wx2hbkq7yhvz0ikhqdv9gp4", "depends": ["GenomeInfoDb", "Hmisc", "S4Vectors", "VariantAnnotation", "httr", "jsonlite", "magrittr", "plyr"] }, "mzID": { "name": "mzID", "version": "1.46.0", "sha256": "0xsk7g3jyqw75lpfa3rw2gg2xg648acrb0klyksb9cac2mhpl4w2", "depends": ["ProtGenerics", "XML", "doParallel", "foreach", "iterators", "plyr"] }, "mzR": { "name": "mzR", "version": "2.42.0", "sha256": "0sm6scdrswxv67yz2kg5n4n4354j9pxxq0bzc6jgkh0y97k6vw9r", "depends": ["Biobase", "BiocGenerics", "ProtGenerics", "Rcpp", "Rhdf5lib", "ncdf4"] }, "ncGTW": { "name": "ncGTW", "version": "1.22.0", "sha256": "008l82ganh0zljmh98q5gq0k44qzilsb4qwnybi7dk8mjbh0pksf", "depends": ["BiocParallel", "Rcpp", "xcms"] }, "ncRNAtools": { "name": "ncRNAtools", "version": "1.18.0", "sha256": "1mlpm8bz5lhqplm5a6k127b2wx5hay6ln5jzz7k2igjyjsrzy0hj", "depends": ["GenomicRanges", "IRanges", "S4Vectors", "ggplot2", "httr", "xml2"] }, "ncdfFlow": { "name": "ncdfFlow", "version": "2.54.0", "sha256": "0b4vriw7msvl0pv7m7wpx3gqg10pfdj6vnclawx2v3zarqbl2ny0", "depends": ["BH", "Biobase", "BiocGenerics", "Rhdf5lib", "cpp11", "flowCore"] }, "ndexr": { "name": "ndexr", "version": "1.30.0", "sha256": "0m1scmqpsha05pixlkq8a5xsfhbvml7knal8wqxvb9x0rzvizqiy", "depends": ["RCX", "httr", "jsonlite", "plyr", "tidyr"] }, "nearBynding": { "name": "nearBynding", "version": "1.18.0", "sha256": "0wh4j84i4vr51kjy9p2p6s3l48xz9vmh4zffqvf655w00n5kmi9a", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "R_utils", "Rsamtools", "S4Vectors", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "dplyr", "ggplot2", "gplots", "magrittr", "matrixStats", "plyranges", "rlang", "rtracklayer", "transport"] }, "nempi": { "name": "nempi", "version": "1.16.0", "sha256": "0kc2ndb7a3nhk64z9pnivrkrhmjskf9xb4aq7b0kig1f5pwf25b8", "depends": ["e1071", "epiNEM", "matrixStats", "mnem", "naturalsort", "nnet", "randomForest"] }, "netSmooth": { "name": "netSmooth", "version": "1.28.0", "sha256": "13i75cdy8w9xixxlm1zkhdpcp5v15n1dc3qp4af6q9jz8a7m1qh7", "depends": ["DelayedArray", "HDF5Array", "Matrix", "SingleCellExperiment", "SummarizedExperiment", "cluster", "clusterExperiment", "data_table", "entropy", "scater"] }, "netboost": { "name": "netboost", "version": "2.16.0", "sha256": "1wlcwvksf5a4ypk1l3lzpik84m83xjcvgg92pfjv28w2n2bi4im6", "depends": ["BiocStyle", "R_utils", "Rcpp", "RcppParallel", "WGCNA", "colorspace", "dynamicTreeCut", "impute"] }, "nethet": { "name": "nethet", "version": "1.40.0", "sha256": "1r9hsgnhmhy2zfha5dqlazdjb4826bl4kw3gr6p4rpzw8f7vp3yl", "depends": ["CompQuadForm", "GSA", "GeneNet", "ICSNP", "ggm", "ggplot2", "glasso", "glmnet", "huge", "limma", "mclust", "multtest", "mvtnorm", "network"] }, "netprioR": { "name": "netprioR", "version": "1.34.0", "sha256": "0i521c4453vdraj6mljpk621zx5avrddz3mpy032wiqsbqlkxknd", "depends": ["Matrix", "doParallel", "dplyr", "foreach", "ggplot2", "gridExtra", "pROC", "sparseMVN"] }, "netresponse": { "name": "netresponse", "version": "1.68.0", "sha256": "03my3rhbl2v6x2d4h0iyc97dck3c79l8lwlp1r2hglr878n8hbld", "depends": ["BiocStyle", "RColorBrewer", "Rgraphviz", "ggplot2", "graph", "igraph", "mclust", "minet", "plyr", "qvalue", "reshape2", "rmarkdown"] }, "ngsReports": { "name": "ngsReports", "version": "2.10.0", "sha256": "1b9ngp2s3xlws0p65qj290ysrgkffrfifxhh70d1l61hxcdvq9gq", "depends": ["BiocGenerics", "Biostrings", "checkmate", "dplyr", "forcats", "ggdendro", "ggplot2", "jsonlite", "lifecycle", "lubridate", "patchwork", "plotly", "reshape2", "rlang", "rmarkdown", "scales", "stringr", "tibble", "tidyr", "tidyselect", "zoo"] }, "nipalsMCIA": { "name": "nipalsMCIA", "version": "1.6.0", "sha256": "02vzhshbv6zk6iriqkypy5hyca1ncpadf5629q2jjz5ry27zlgjy", "depends": ["ComplexHeatmap", "MultiAssayExperiment", "RSpectra", "SummarizedExperiment", "dplyr", "fgsea", "ggplot2", "pracma", "rlang", "scales"] }, "nnNorm": { "name": "nnNorm", "version": "2.72.0", "sha256": "0g43lyri5mzk6r755rc1gf2vz18g8x51ang9f9svjr0yf34zrspp", "depends": ["marray", "nnet"] }, "nnSVG": { "name": "nnSVG", "version": "1.12.0", "sha256": "13lvwhfxrdfp00h7b8j6swnayyxly8gcicwhdmam4d30vpqgf711", "depends": ["BRISC", "BiocParallel", "Matrix", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "matrixStats"] }, "nondetects": { "name": "nondetects", "version": "2.38.1", "sha256": "19jzd2yinjgqawk4ay1ywwlyw5q9yhrp3pa12z1w0caprxzxddkx", "depends": ["Biobase", "HTqPCR", "arm", "limma", "mvtnorm"] }, "normalize450K": { "name": "normalize450K", "version": "1.36.0", "sha256": "1ga00yhznki6gw532bzz9bkgbak39lq4yfplnry3wja0930xw3v3", "depends": ["Biobase", "illuminaio", "quadprog"] }, "normr": { "name": "normr", "version": "1.34.0", "sha256": "15f465yxmcp7lxv5rjaji99jqa84s4f9k2vjfj0qdc9fmijxq3l8", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "Rcpp", "bamsignals", "qvalue", "rtracklayer"] }, "npGSEA": { "name": "npGSEA", "version": "1.44.0", "sha256": "1lkpvbizdq0wzdfn30vcynfhx01wch1yki3zzzkqgjgyhsjaqfn1", "depends": ["Biobase", "BiocGenerics", "GSEABase"] }, "nuCpos": { "name": "nuCpos", "version": "1.26.0", "sha256": "1swkykv34aalwhk6wr6d4ja1h9yl1rx6ys3f81vk6r1wsqi1rs9l", "depends": [] }, "nucleR": { "name": "nucleR", "version": "2.40.0", "sha256": "1n0nxqx7hnnn74wp3l02bfl2fkc1c4ak0lnyh7cd45018ygs76fd", "depends": ["Biobase", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "ShortRead", "dplyr", "ggplot2", "magrittr"] }, "nucleoSim": { "name": "nucleoSim", "version": "1.36.0", "sha256": "1hydk3ay021g6m94i217prrb54r8prh14idflljjjrqx3jpf57ma", "depends": ["IRanges", "S4Vectors"] }, "nullranges": { "name": "nullranges", "version": "1.14.0", "sha256": "1458p8r4mmfvp75xi3j47d615dx285sy32vr0hjhvwqfwkkz3p8d", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "InteractionSet", "S4Vectors", "data_table", "ggplot2", "ggridges", "plyranges", "progress", "rlang", "scales"] }, "occugene": { "name": "occugene", "version": "1.68.0", "sha256": "0y5wj927gy938vnv5irj9n1a12rfbfq2m2q3zpny0rd390bdpxmc", "depends": [] }, "octad": { "name": "octad", "version": "1.9.0", "sha256": "1w4nc2n1a93268bg3l3bhas48bsr6hlp5g4947xryr3b4dgc6dxb", "depends": ["AnnotationHub", "Biobase", "DESeq2", "EDASeq", "ExperimentHub", "GSVA", "RUVSeq", "Rfast", "S4Vectors", "data_table", "dplyr", "edgeR", "foreach", "ggplot2", "htmlwidgets", "httr", "limma", "magrittr", "octad_db", "plotly", "qpdf", "reshape2", "rhdf5"] }, "odseq": { "name": "odseq", "version": "1.36.0", "sha256": "08yr4448ij8jh6kzxq9sn7zv2xp0cjzvlllzz47x18v0py466vp8", "depends": ["kebabs", "mclust", "msa"] }, "oligo": { "name": "oligo", "version": "1.72.0", "sha256": "1f57jzfsrz3fx3z0w97pgipcrjspw08y32v4r7r22yiywlxbksa2", "depends": ["Biobase", "BiocGenerics", "Biostrings", "DBI", "RSQLite", "affxparser", "affyio", "bit", "ff", "oligoClasses", "preprocessCore"] }, "oligoClasses": { "name": "oligoClasses", "version": "1.70.0", "sha256": "04357ab8jx7vqj8k82q6j05z74pwayvgmxb8r1rw67zq6z6v6r02", "depends": ["Biobase", "BiocGenerics", "BiocManager", "Biostrings", "DBI", "GenomicRanges", "IRanges", "RSQLite", "S4Vectors", "SummarizedExperiment", "affyio", "ff", "foreach"] }, "omXplore": { "name": "omXplore", "version": "1.2.2", "sha256": "0x9ag6brzimbfddi5v6q60bhp57zvrpkhk8cc2shzbm1j11fhnyn", "depends": ["DT", "FactoMineR", "MSnbase", "MultiAssayExperiment", "PSMatch", "RColorBrewer", "SummarizedExperiment", "dendextend", "dplyr", "factoextra", "gplots", "highcharter", "htmlwidgets", "nipals", "shiny", "shinyBS", "shinyjqui", "shinyjs", "tibble", "tidyr", "vioplot", "visNetwork"] }, "omada": { "name": "omada", "version": "1.10.0", "sha256": "13ywxl0z6nklga23r8lhdnk1zpcd6c62jr5giy9j72hp42c6dvva", "depends": ["Rcpp", "clValid", "diceR", "dplyr", "fpc", "genieclust", "ggplot2", "glmnet", "kernlab", "pdfCluster", "reshape"] }, "omicRexposome": { "name": "omicRexposome", "version": "1.30.0", "sha256": "0km7bg018i5g0l98ygrw0f4m753h0l1klgjkbnsv6wnyy7xqczaf", "depends": ["Biobase", "MultiDataSet", "PMA", "SmartSVA", "SummarizedExperiment", "ggplot2", "ggrepel", "gridExtra", "isva", "limma", "omicade4", "rexposome", "stringr", "sva"] }, "omicade4": { "name": "omicade4", "version": "1.48.0", "sha256": "0rr2mnhilb5badrp3flb2sv39f9365i30kb5053lif0gc5m7r5rg", "depends": ["Biobase", "ade4", "made4"] }, "omicplotR": { "name": "omicplotR", "version": "1.28.0", "sha256": "1vbarxn0p2n2mdr6vdadw6xv2lb4pp6nvlmyii7r9rxhbbp88wi7", "depends": ["ALDEx2", "DT", "compositions", "jsonlite", "knitr", "matrixStats", "rmarkdown", "shiny", "vegan", "zCompositions"] }, "omicsPrint": { "name": "omicsPrint", "version": "1.28.0", "sha256": "1w8birg6p9vw59sl1q5za5nrnwfjcb88sbn6afc9g9vz8y5v85wz", "depends": ["MASS", "MultiAssayExperiment", "RaggedExperiment", "SummarizedExperiment", "matrixStats"] }, "omicsViewer": { "name": "omicsViewer", "version": "1.12.0", "sha256": "137cjryzwgkl91qjm85q1rk6hn5xz6y8m046wmdlxk7aq6pjw9bf", "depends": ["Biobase", "DT", "Matrix", "RColorBrewer", "ROCR", "RSQLite", "S4Vectors", "SummarizedExperiment", "beeswarm", "curl", "drc", "fastmatch", "fgsea", "flatxml", "ggplot2", "ggseqlogo", "htmlwidgets", "httr", "matrixStats", "networkD3", "openxlsx", "plotly", "psych", "reshape2", "shiny", "shinyWidgets", "shinybusy", "shinycssloaders", "shinyjs", "shinythemes", "stringr", "survival", "survminer"] }, "ompBAM": { "name": "ompBAM", "version": "1.12.0", "sha256": "0i9szx0b4xq94k0vzb1dqwrb3b25hx54d1l8dkk75hdscb0rbjp2", "depends": ["Rcpp"] }, "oncomix": { "name": "oncomix", "version": "1.30.0", "sha256": "1yps1188z3bm4phhmj3hcb1bf4qgq8g552c42jxcvfprkrphabzd", "depends": ["RColorBrewer", "SummarizedExperiment", "ggplot2", "ggrepel", "mclust"] }, "oncoscanR": { "name": "oncoscanR", "version": "1.10.0", "sha256": "1bshhqzxqpydgvwj7bb609fvw54133h01z1mi26z4nxwkdark9vw", "depends": ["GenomicRanges", "IRanges", "S4Vectors", "magrittr", "readr"] }, "onlineFDR": { "name": "onlineFDR", "version": "2.16.0", "sha256": "1nn51bykaciy2crnrm5z1b4rpx8083hxjxzcjx1q4fylwfxpr9hj", "depends": ["Rcpp", "RcppProgress", "progress"] }, "ontoProc": { "name": "ontoProc", "version": "2.2.1", "sha256": "050lg114ygfli28a6shc3r2aqn01vdja8dyaxm0hsavq9jslpf5s", "depends": ["AnnotationHub", "Biobase", "BiocFileCache", "DT", "R_utils", "Rgraphviz", "S4Vectors", "SummarizedExperiment", "basilisk", "dplyr", "graph", "httr", "igraph", "magrittr", "ontologyIndex", "ontologyPlot", "reticulate", "shiny"] }, "openCyto": { "name": "openCyto", "version": "2.20.0", "sha256": "18z446ggvrmgicnyyfg1qd3xp62rz29125dfwrihz325px8rjsiy", "depends": ["BH", "Biobase", "BiocGenerics", "RBGL", "RColorBrewer", "cpp11", "data_table", "flowClust", "flowCore", "flowViz", "flowWorkspace", "graph", "ncdfFlow"] }, "openPrimeR": { "name": "openPrimeR", "version": "1.30.1", "sha256": "1yz39y7902qhb1yjrzzj7c0qkq9pld4wf352sb1p2dkxs8cr7qm5", "depends": ["BiocGenerics", "Biostrings", "DECIPHER", "GenomicRanges", "Hmisc", "IRanges", "RColorBrewer", "S4Vectors", "XML", "ape", "digest", "dplyr", "foreach", "ggplot2", "lpSolveAPI", "magrittr", "openxlsx", "plyr", "pwalign", "reshape2", "scales", "seqinr", "stringdist", "stringr", "uniqtag"] }, "oposSOM": { "name": "oposSOM", "version": "2.26.0", "sha256": "07c4832hb5ib4cqj8sqsacw5r4vqnv2q6vphi0v7c5nd95jc8crx", "depends": ["Biobase", "RCurl", "Rcpp", "RcppParallel", "XML", "ape", "biomaRt", "fastICA", "fdrtool", "graph", "igraph", "pixmap", "png", "scatterplot3d", "tsne"] }, "oppar": { "name": "oppar", "version": "1.36.1", "sha256": "0f5y093sr0jdkrm95ib6y1jszw8m7r3jkbd9a6qfhki8rzqwsavk", "depends": ["Biobase", "GSEABase", "GSVA"] }, "oppti": { "name": "oppti", "version": "1.21.0", "sha256": "0v7hy9qy3mjx8sj3rvs23sy38r8nfgr4d4na4k8h65y2mi8xfqnp", "depends": ["RColorBrewer", "devtools", "ggplot2", "knitr", "limma", "parallelDist", "pheatmap", "reshape"] }, "optimalFlow": { "name": "optimalFlow", "version": "1.20.0", "sha256": "0abr0c8x92d9p3q4k8a53ij355xz6pjp3yx1f5dqxhq12by4f7zr", "depends": ["Rfast", "dbscan", "doParallel", "dplyr", "ellipse", "flowMeans", "foreach", "optimalFlowData", "randomForest", "rgl", "rlang", "robustbase", "transport"] }, "orthogene": { "name": "orthogene", "version": "1.14.0", "sha256": "0v6y1ih476spnvmbhnrbwiglpcapcg7a61min8jib89prhsqhvbi", "depends": ["DelayedArray", "Matrix", "babelgene", "data_table", "dplyr", "ggplot2", "ggpubr", "ggtree", "gprofiler2", "grr", "homologene", "jsonlite", "patchwork", "repmis"] }, "orthos": { "name": "orthos", "version": "1.6.0", "sha256": "0f742pna8d3iys5sgyzwj1hlj00hqjsgnnzs1pj8rbk1clzdwipp", "depends": ["AnnotationHub", "BiocParallel", "DelayedArray", "ExperimentHub", "HDF5Array", "S4Vectors", "SummarizedExperiment", "basilisk", "colorspace", "cowplot", "dplyr", "ggplot2", "ggpubr", "ggrepel", "ggsci", "keras", "orthosData", "plyr", "reticulate", "rlang", "tensorflow", "tidyr"] }, "pRoloc": { "name": "pRoloc", "version": "1.48.0", "sha256": "10mr8k1zvh80ah142zzw0x31b34f0563ydg46mcmwh9q2k45ms3v", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "FNN", "LaplacesDemon", "MASS", "MLInterfaces", "MSnbase", "RColorBrewer", "Rcpp", "RcppArmadillo", "biomaRt", "caret", "class", "coda", "colorspace", "dendextend", "e1071", "ggplot2", "gtools", "hexbin", "kernlab", "knitr", "lattice", "mclust", "mixtools", "mvtnorm", "nnet", "plyr", "proxy", "randomForest", "sampling", "scales"] }, "pRolocGUI": { "name": "pRolocGUI", "version": "2.18.0", "sha256": "1094vsjxknkj9w30zikllb7kb0w8k7l7nb4agjisabc3dzsk9jwc", "depends": ["Biobase", "BiocGenerics", "DT", "MSnbase", "colorspace", "colourpicker", "dplyr", "ggplot2", "pRoloc", "scales", "shiny", "shinyWidgets", "shinydashboard", "shinydashboardPlus", "shinyhelper", "shinyjs"] }, "packFinder": { "name": "packFinder", "version": "1.20.0", "sha256": "02bf2454nspyndz79xk1s9g452q5aswivb7p1njxrfscm73hr4g7", "depends": ["Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "ape", "kmer"] }, "padma": { "name": "padma", "version": "1.18.1", "sha256": "0rzgly9g2qmhksiazy4nsn2s4vfznxdpsi00gcj1pd4cfwlkvj2s", "depends": ["FactoMineR", "MultiAssayExperiment", "S4Vectors", "SummarizedExperiment"] }, "pageRank": { "name": "pageRank", "version": "1.18.0", "sha256": "134yd2gl84yj3sa8xb9xsijv454wq8w1xvs13nkf0lvcq3szw192", "depends": ["GenomicRanges", "igraph", "motifmatchr"] }, "paircompviz": { "name": "paircompviz", "version": "1.46.0", "sha256": "0flb0i3j35r7a3xl99vc6xn4lkwa5mdvs2l6mly8d8kpbqlcz2w2", "depends": ["Rgraphviz"] }, "pairedGSEA": { "name": "pairedGSEA", "version": "1.8.0", "sha256": "07rcdk8z8lz108rcn6hhyp8j068kcpiszqh402p68kfij3rp40yn", "depends": ["BiocParallel", "DESeq2", "DEXSeq", "S4Vectors", "SummarizedExperiment", "aggregation", "fgsea", "ggplot2", "limma", "msigdbr", "showtext", "sva"] }, "pairkat": { "name": "pairkat", "version": "1.14.0", "sha256": "1mz12l5dp56yv4j6risnxzrjcva2f9rhii0ssz7nig92c25qnqby", "depends": ["CompQuadForm", "KEGGREST", "SummarizedExperiment", "data_table", "igraph", "magrittr", "tibble"] }, "pandaR": { "name": "pandaR", "version": "1.40.0", "sha256": "05s525kndwb86lhkq3ja8aywgazvr0k246gi47602bgi7g2byli2", "depends": ["Biobase", "BiocGenerics", "RUnit", "ggplot2", "hexbin", "igraph", "matrixStats", "plyr", "reshape"] }, "panelcn_mops": { "name": "panelcn.mops", "version": "1.30.0", "sha256": "02zfcb5bjz5nmi85pwxm7wr3wnapq6l9abfn8ps263w9gnm55si4", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "cn_mops"] }, "panp": { "name": "panp", "version": "1.78.0", "sha256": "04qf5188flaaypdf22ysqhpcjpj2vp1lc4n2hx4rc3s4lxv2pff4", "depends": ["Biobase", "affy"] }, "parglms": { "name": "parglms", "version": "1.40.0", "sha256": "0cbcbngfl5r4srjib7ihnxycgvvr9kz5q53d17wkagsmqvfvgmvv", "depends": ["BatchJobs", "BiocGenerics", "doParallel", "foreach"] }, "parody": { "name": "parody", "version": "1.66.1", "sha256": "064pr73zbx3008khmnif7frxdhgbmarbzqa82lzmvzh4a5ldr15z", "depends": [] }, "partCNV": { "name": "partCNV", "version": "1.6.0", "sha256": "0p8ci8c9rw30kcrcrc4pkzvkcnsdn1w2ph4zx8lzfwz0lsy62qha", "depends": ["AnnotationHub", "BiocStyle", "GenomicRanges", "Seurat", "SingleCellExperiment", "data_table", "depmixS4", "magrittr"] }, "pathMED": { "name": "pathMED", "version": "1.0.2", "sha256": "1v36dah8pd6fxwnyp89qlpnbd5cxq86ndk9l7bwrwri6p17kgrgy", "depends": ["BiocParallel", "FactoMineR", "GSVA", "caret", "caretEnsemble", "decoupleR", "dplyr", "factoextra", "ggplot2", "magrittr", "matrixStats", "metrica", "pbapply", "reshape2", "singscore", "stringi"] }, "pathRender": { "name": "pathRender", "version": "1.76.0", "sha256": "19z5gpfnv9c1rq4gdm3g7giwpipcrayac37cnjw5apxy81klqdpg", "depends": ["AnnotationDbi", "RColorBrewer", "Rgraphviz", "cMAP", "graph"] }, "pathifier": { "name": "pathifier", "version": "1.46.0", "sha256": "1hh63mrm90981xd7vyhlfr1bsxb4jkvl48x4bp38alfmnih75kmv", "depends": ["R_oo", "princurve"] }, "pathlinkR": { "name": "pathlinkR", "version": "1.4.0", "sha256": "1wn1h64vgs8vc9knjw0f57ssqvdxyspq09v492y9yjz2j3d1zaid", "depends": ["ComplexHeatmap", "circlize", "clusterProfiler", "dplyr", "fgsea", "ggforce", "ggplot2", "ggpubr", "ggraph", "ggrepel", "igraph", "purrr", "sigora", "stringr", "tibble", "tidygraph", "tidyr", "vegan", "visNetwork"] }, "pathview": { "name": "pathview", "version": "1.48.0", "sha256": "096nf0p69jyj5ih09r1azz3ia5dzjj2n871kfmmm80sdzi1qs04g", "depends": ["AnnotationDbi", "KEGGREST", "KEGGgraph", "Rgraphviz", "XML", "graph", "org_Hs_eg_db", "png"] }, "pathwayPCA": { "name": "pathwayPCA", "version": "1.24.0", "sha256": "1ksga0fz3pxd7kax3sngbfps3vr0kihc06b0fwnf37hgqs0svyzv", "depends": ["lars", "survival"] }, "pcaExplorer": { "name": "pcaExplorer", "version": "3.2.0", "sha256": "0scm0f8j85q74fscj77pgpkcysy3vhmz4mhxw5yhvf89gw5z6z92", "depends": ["AnnotationDbi", "DESeq2", "DT", "GO_db", "GOstats", "GenomicRanges", "IRanges", "NMF", "S4Vectors", "SummarizedExperiment", "base64enc", "biomaRt", "genefilter", "ggplot2", "ggrepel", "heatmaply", "knitr", "limma", "mosdef", "pheatmap", "plotly", "plyr", "rmarkdown", "scales", "shiny", "shinyAce", "shinyBS", "shinydashboard", "threejs", "tidyr", "topGO"] }, "pcaMethods": { "name": "pcaMethods", "version": "2.0.0", "sha256": "10rzf1anac8za7v71s5sliw1dvvazsa8m3vxwf23h053yzndfx84", "depends": ["Biobase", "BiocGenerics", "MASS", "Rcpp"] }, "pdInfoBuilder": { "name": "pdInfoBuilder", "version": "1.72.0", "sha256": "1rqsvp66xqvwh2axai2063yd1gdqdfb3pd0zw7hrjhw4f97hagmz", "depends": ["Biobase", "BiocGenerics", "Biostrings", "DBI", "IRanges", "RSQLite", "S4Vectors", "affxparser", "oligo", "oligoClasses"] }, "peakPantheR": { "name": "peakPantheR", "version": "1.22.0", "sha256": "04ixkcnwhb3677099wx58sjrdg2v6gmr592i916gskfzkk40pk62", "depends": ["DT", "MSnbase", "XML", "bslib", "doParallel", "foreach", "ggplot2", "gridExtra", "lubridate", "minpack_lm", "mzR", "pracma", "scales", "shiny", "shinycssloaders", "stringr", "svglite"] }, "peco": { "name": "peco", "version": "1.20.0", "sha256": "11a85jrzpkw1rfmzjzx7cw41vvqa883qss7i8fy5qap01rsks3wn", "depends": ["SingleCellExperiment", "SummarizedExperiment", "assertthat", "circular", "conicfit", "doParallel", "foreach", "genlasso", "scater"] }, "pengls": { "name": "pengls", "version": "1.14.0", "sha256": "06ivyncvlrvrw48dkzvx6q81jq5m3nv9p2vif338a6jbh732qppb", "depends": ["BiocParallel", "glmnet", "nlme"] }, "pepStat": { "name": "pepStat", "version": "1.42.0", "sha256": "1ka22y3lkzsvpxxxpi9fdn9lgngwlh2b5gpijng2nfqazppam9x0", "depends": ["Biobase", "GenomicRanges", "IRanges", "data_table", "fields", "ggplot2", "limma", "plyr"] }, "pepXMLTab": { "name": "pepXMLTab", "version": "1.42.0", "sha256": "0j2qp5alanyjxjhwgclw6p2danvh6kkblxzp3ibfk3c02qha7sf3", "depends": ["XML"] }, "periodicDNA": { "name": "periodicDNA", "version": "1.18.0", "sha256": "175lysjyjgw7md5ch0q09k41ak28f3f4lxiv8gnq4ds5f7p9chi8", "depends": ["BSgenome", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "cowplot", "ggplot2", "magrittr", "rtracklayer", "zoo"] }, "pfamAnalyzeR": { "name": "pfamAnalyzeR", "version": "1.8.0", "sha256": "0q5gcq5rm6az62mlhpbg6rawszdpckc5w5kl53bda9gfdcl6bi4l", "depends": ["dplyr", "magrittr", "readr", "stringr", "tibble"] }, "pgca": { "name": "pgca", "version": "1.32.0", "sha256": "12kmjzsasr3y2ghk101bwjx48nls5axr2ggl4agg57zw0231rfgb", "depends": [] }, "pgxRpi": { "name": "pgxRpi", "version": "1.4.3", "sha256": "0pzkc96dvlsfggnk8yz5f1cw9ydzr7parn1aqc313pl9v74r61p2", "depends": ["GenomicRanges", "S4Vectors", "SummarizedExperiment", "attempt", "circlize", "dplyr", "future", "future_apply", "ggplot2", "httr", "lubridate", "survival", "survminer", "yaml"] }, "phantasus": { "name": "phantasus", "version": "1.28.0", "sha256": "1daqcqfp1qdix9dq2ska9759k7madqr3lm02fmmz4388l6svzkgw", "depends": ["AnnotationDbi", "Biobase", "DESeq2", "GEOquery", "Matrix", "Rook", "XML", "apeglm", "assertthat", "ccaPP", "config", "curl", "data_table", "edgeR", "fgsea", "fs", "ggplot2", "gtable", "htmltools", "httpuv", "httr", "jsonlite", "limma", "opencpu", "phantasusLite", "pheatmap", "protolite", "rhdf5", "rhdf5client", "scales", "stringr", "svglite", "tidyr", "yaml"] }, "phantasusLite": { "name": "phantasusLite", "version": "1.6.0", "sha256": "03wnpcn4chh7p75ksgrmsj01n4n98mkrbflvh2znsl2ls6y68lxl", "depends": ["Biobase", "data_table", "httr", "rhdf5client", "stringr"] }, "phenoTest": { "name": "phenoTest", "version": "1.56.0", "sha256": "1gzi5mk4z99a4g60wp5rlzbrfbj57h0wn05a06lqprzvc4r6100i", "depends": ["AnnotationDbi", "BMA", "Biobase", "Category", "GSEABase", "Heatplus", "Hmisc", "annotate", "biomaRt", "ellipse", "genefilter", "ggplot2", "gplots", "hgu133a_db", "hopach", "limma", "mgcv", "survival", "xtable"] }, "phenomis": { "name": "phenomis", "version": "1.10.0", "sha256": "08zlqipfr5mnw2f3xslchbws2s9irwnsjbkb09zkn6ckddykjfb1", "depends": ["Biobase", "MultiAssayExperiment", "MultiDataSet", "PMCMRplus", "RColorBrewer", "SummarizedExperiment", "VennDiagram", "biodb", "biodbChebi", "data_table", "futile_logger", "ggplot2", "ggrepel", "htmlwidgets", "igraph", "limma", "plotly", "ranger", "ropls", "tibble", "tidyr"] }, "phenopath": { "name": "phenopath", "version": "1.32.0", "sha256": "17l0av4hpcam3qs6rwsrd8a3195k2gxp5nqw1hcicz9vjsr6a9zv", "depends": ["Rcpp", "SummarizedExperiment", "dplyr", "ggplot2", "tibble", "tidyr"] }, "philr": { "name": "philr", "version": "1.34.0", "sha256": "1gqzw8hfvgkcds80fmv0dr9hgyq1qqq21rmg4d1hrm91h0m29wma", "depends": ["ape", "ggplot2", "ggtree", "phangorn", "tidyr"] }, "phosphonormalizer": { "name": "phosphonormalizer", "version": "1.32.0", "sha256": "03bnqkmn4b34cj987i4sd90bgwffy38vgzid9fnacr701ybnc6c9", "depends": ["matrixStats", "plyr"] }, "phyloseq": { "name": "phyloseq", "version": "1.52.0", "sha256": "0yrfskwv5vah20ynrpxxk4fizxc2z8j86lkhldwd4yfkwkc1nsir", "depends": ["Biobase", "BiocGenerics", "Biostrings", "ade4", "ape", "biomformat", "cluster", "data_table", "foreach", "ggplot2", "igraph", "multtest", "plyr", "reshape2", "scales", "vegan"] }, "piano": { "name": "piano", "version": "2.24.0", "sha256": "116fy2jmgy73fh080w6rzfzb0m2icvl8k5z2vcc3mf6p43kpkf2w", "depends": ["Biobase", "BiocGenerics", "DT", "fgsea", "gplots", "htmlwidgets", "igraph", "marray", "relations", "scales", "shiny", "shinydashboard", "shinyjs", "visNetwork"] }, "pickgene": { "name": "pickgene", "version": "1.80.0", "sha256": "1vg4bc2sf2d8rgps4qlv5nzj4p7p55hwhp657vgwc3famhd9ickj", "depends": ["MASS"] }, "pipeComp": { "name": "pipeComp", "version": "1.18.0", "sha256": "1bryavymna9sfx40fwrgr6s5pf0rarxdq7ydik3nr56r3fx06y6j", "depends": ["BiocParallel", "ComplexHeatmap", "Matrix", "RColorBrewer", "Rtsne", "S4Vectors", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "aricode", "circlize", "clue", "cluster", "cowplot", "dplyr", "ggplot2", "intrinsicDimension", "knitr", "matrixStats", "randomcoloR", "reshape2", "scales", "scater", "scran", "uwot", "viridisLite"] }, "pipeFrame": { "name": "pipeFrame", "version": "1.24.0", "sha256": "0qckysswmfbw6gqq9a7fln9c6m97z310a7x9j5l8a8kpbzn6hn7m", "depends": ["BSgenome", "Biostrings", "GenomeInfoDb", "digest", "magrittr", "rmarkdown", "visNetwork"] }, "planet": { "name": "planet", "version": "1.16.0", "sha256": "0347kl1x7f7sm4szsqnjl8ahnxfhr6zmzvchsyp223svvsdzf5hq", "depends": ["dplyr", "magrittr", "tibble"] }, "planttfhunter": { "name": "planttfhunter", "version": "1.8.0", "sha256": "0wnwm31fzfzg710217kcbhq1gd2d9187qb3p6ghxksbl15wg1cx8", "depends": ["Biostrings", "SummarizedExperiment"] }, "plasmut": { "name": "plasmut", "version": "1.6.0", "sha256": "0igv0f8x3sxnw9ryi8hvci7l36qv8xqxr9gh2byrz6giwhiis2gp", "depends": ["dplyr", "tibble"] }, "plgem": { "name": "plgem", "version": "1.80.0", "sha256": "0mc4kpbnvbs5a1bgrnmwa58kfbdpx3a7sacjacnn1k44s6smdmbw", "depends": ["Biobase", "MASS"] }, "plier": { "name": "plier", "version": "1.78.0", "sha256": "0vacscadv6adi3qgb3zcjb7380i9ygp2pv1mbclfkr855xfwfqz4", "depends": ["Biobase", "affy"] }, "plotGrouper": { "name": "plotGrouper", "version": "1.26.0", "sha256": "0485m3hd0lckq2mp99l6aa6w0mg8nvjnp3774k3ch4xp5cx5cds6", "depends": ["Hmisc", "colourpicker", "dplyr", "egg", "ggplot2", "ggpubr", "gridExtra", "gtable", "magrittr", "readr", "readxl", "rlang", "scales", "shiny", "shinythemes", "stringr", "tibble", "tidyr"] }, "plotgardener": { "name": "plotgardener", "version": "1.14.0", "sha256": "13dg2rr8wy4mvjwc66cl7xs8fhs3hbbhy2x4fjd89nkpihfn14c7", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "Rcpp", "curl", "data_table", "dplyr", "ggplotify", "glue", "plyranges", "purrr", "rhdf5", "rlang", "strawr", "withr"] }, "plyinteractions": { "name": "plyinteractions", "version": "1.6.0", "sha256": "1gspylz6d3jlynf4waqsi4ra28jsvc7202fgv17i21yd7mcx7v0w", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "InteractionSet", "S4Vectors", "dplyr", "plyranges", "rlang", "tibble", "tidyselect"] }, "plyranges": { "name": "plyranges", "version": "1.28.0", "sha256": "08iif4rllnshp3xzsk8y08c3jnpk2k4bbnf6f7rsx2q4sgvnlcpn", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "dplyr", "magrittr", "rlang", "rtracklayer", "tidyselect"] }, "plyxp": { "name": "plyxp", "version": "1.2.7", "sha256": "03c469y98jfwk48alfky18mpb9dmh57cahkp42dgdfr8pvdknx2p", "depends": ["S4Vectors", "S7", "SummarizedExperiment", "cli", "dplyr", "glue", "pillar", "purrr", "rlang", "tibble", "tidyr", "tidyselect", "vctrs"] }, "pmm": { "name": "pmm", "version": "1.40.0", "sha256": "145jpp9fh7m1aw1rc1wdvg4a6s0aws9f48vz6p770n9x0s6nc1la", "depends": ["lme4"] }, "pmp": { "name": "pmp", "version": "1.20.0", "sha256": "0404ap89a74s8a1p9k98c44ai189jgh987l89b78jh9cgi4bs2k6", "depends": ["S4Vectors", "SummarizedExperiment", "ggplot2", "impute", "matrixStats", "missForest", "pcaMethods", "reshape2"] }, "podkat": { "name": "podkat", "version": "1.40.0", "sha256": "0vg46rjs6k7byvchhfs541p083v4klp1n7gci2q0ny6yckr0fc4w", "depends": ["BSgenome", "Biobase", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "Matrix", "Rcpp", "Rhtslib", "Rsamtools"] }, "poem": { "name": "poem", "version": "1.0.1", "sha256": "09dmzdhgfzi7mhfxhx9fairkvr1qxskdlp9igf590r5wyb42lagf", "depends": ["BiocNeighbors", "BiocParallel", "Matrix", "SpatialExperiment", "SummarizedExperiment", "aricode", "bluster", "clevr", "clue", "cluster", "elsa", "fclust", "igraph", "matrixStats", "mclustcomp", "pdist", "sp", "spdep"] }, "pogos": { "name": "pogos", "version": "1.28.0", "sha256": "19jsl6993zq5nl32zhkjsa6kwmn2ggzbhmbysmxq8al7vavpgyb0", "depends": ["S4Vectors", "ggplot2", "httr", "ontoProc", "rjson", "shiny"] }, "powerTCR": { "name": "powerTCR", "version": "1.28.0", "sha256": "06xbsbvhafm442b1kjyw1k05nap4wpwcdipgiclkb972nlmrm1i4", "depends": ["VGAM", "cubature", "doParallel", "evmix", "foreach", "magrittr", "purrr", "truncdist", "vegan"] }, "ppcseq": { "name": "ppcseq", "version": "1.16.0", "sha256": "0wxzkhky14hz02k85ghvq6qcjs5j95yi716sqw1b9j7aifb6c9wv", "depends": ["BH", "Rcpp", "RcppEigen", "RcppParallel", "StanHeaders", "benchmarkme", "dplyr", "edgeR", "foreach", "ggplot2", "lifecycle", "magrittr", "purrr", "rlang", "rstan", "rstantools", "tibble", "tidybayes", "tidyr"] }, "pqsfinder": { "name": "pqsfinder", "version": "2.24.0", "sha256": "0az362s402w0khcsb5zn2hza60q0kpdmcn86dci8kfv0xn340msr", "depends": ["BH", "Biostrings", "GenomicRanges", "IRanges", "Rcpp", "S4Vectors"] }, "pram": { "name": "pram", "version": "1.24.0", "sha256": "0dzq90wziq0mksb1q4kiphgqq3f1pzx1za5ldwz47cndsccimmhq", "depends": ["BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "data_table", "rtracklayer"] }, "prebs": { "name": "prebs", "version": "1.48.0", "sha256": "092hc5pppcqshjp4497rz0z84lb811if9ra18dsh5ggs9p79d114", "depends": ["Biobase", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "RPA", "S4Vectors", "affy"] }, "preciseTAD": { "name": "preciseTAD", "version": "1.18.0", "sha256": "14qq3zgrfac7ysj2jclcig0dfhj8rc8cwvxpbby75akwm1024qw5", "depends": ["GenomicRanges", "IRanges", "ModelMetrics", "PRROC", "S4Vectors", "caret", "cluster", "dbscan", "doSNOW", "e1071", "foreach", "gtools", "pROC", "pbapply", "rCGH", "randomForest"] }, "preprocessCore": { "name": "preprocessCore", "version": "1.70.0", "sha256": "062ymdjc48580yv1kl36p0prvffk8qcf5ypsvdvdqikxfp6ayrvp", "depends": [] }, "primirTSS": { "name": "primirTSS", "version": "1.26.0", "sha256": "0h188r0a16cfd8482jpa1qk33hj9l9f5gp3hlsb2hbfyg6l4ib36", "depends": ["BSgenome_Hsapiens_UCSC_hg38", "BiocGenerics", "Biostrings", "GenomicRanges", "GenomicScores", "Gviz", "IRanges", "JASPAR2018", "R_utils", "S4Vectors", "TFBSTools", "dplyr", "phastCons100way_UCSC_hg38", "purrr", "rtracklayer", "shiny", "stringr", "tibble", "tidyr"] }, "proActiv": { "name": "proActiv", "version": "1.18.0", "sha256": "0x4lgd3rv0r4dj4b0rfpafj1sznd56h8mf99x8rava9lhv2j94jm", "depends": ["AnnotationDbi", "BiocParallel", "DESeq2", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "data_table", "dplyr", "ggplot2", "gplots", "rlang", "scales", "tibble", "txdbmaker"] }, "proBAMr": { "name": "proBAMr", "version": "1.42.0", "sha256": "0cywq08np6lxbbs1nc2grgcq99g184855zq1jg3xj3ah3qfgj9r8", "depends": ["AnnotationDbi", "Biostrings", "GenomicFeatures", "GenomicRanges", "IRanges", "rtracklayer", "txdbmaker"] }, "proDA": { "name": "proDA", "version": "1.22.1", "sha256": "0cdk8kjirinj8f6zvpvnnncsm2rkla82ld998lcm4fx2mmglsmrm", "depends": ["BiocGenerics", "S4Vectors", "SummarizedExperiment", "extraDistr"] }, "procoil": { "name": "procoil", "version": "2.36.0", "sha256": "0iwkngssiavx6fvx6w9g56hr6yrfn2j4k2j0lzhwzb1pjq2wwdv4", "depends": ["Biostrings", "S4Vectors", "kebabs"] }, "profileScoreDist": { "name": "profileScoreDist", "version": "1.36.0", "sha256": "1700vq8lmhkza6g092szblbcfvb5wi93a319zlz3r7jzlsycqjna", "depends": ["BiocGenerics", "Rcpp"] }, "profileplyr": { "name": "profileplyr", "version": "1.24.1", "sha256": "02y423r6g9bi7g5izvrwmxmrxrkyah8496pdrm1xhq97i9k8pdba", "depends": ["BiocGenerics", "BiocParallel", "ChIPseeker", "ComplexHeatmap", "EnrichedHeatmap", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "R_utils", "Rsamtools", "S4Vectors", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "TxDb_Mmusculus_UCSC_mm10_knownGene", "TxDb_Mmusculus_UCSC_mm9_knownGene", "circlize", "dplyr", "ggplot2", "magrittr", "org_Hs_eg_db", "org_Mm_eg_db", "pheatmap", "rGREAT", "rjson", "rlang", "rtracklayer", "soGGi", "tidyr", "tiff"] }, "progeny": { "name": "progeny", "version": "1.30.0", "sha256": "1xxh46d9x2n1naw3m8nn3kdxpjv75mmlpgbpflfhyasf9p67qkjg", "depends": ["Biobase", "decoupleR", "dplyr", "ggplot2", "ggrepel", "gridExtra", "reshape2", "tidyr"] }, "projectR": { "name": "projectR", "version": "1.24.0", "sha256": "14gi5b1mwmnsdvfbly2k0agdv8kax0vlb9vgrf2qa12ds8nhxkvs", "depends": ["Matrix", "MatrixModels", "NMF", "RColorBrewer", "ROCR", "SingleCellExperiment", "cluster", "cowplot", "dplyr", "fgsea", "ggalluvial", "ggplot2", "ggrepel", "limma", "msigdbr", "reshape2", "scales", "tsne", "umap", "viridis"] }, "protGear": { "name": "protGear", "version": "1.12.0", "sha256": "0gnm22iybssn4d3vajbnb67065ahnprsdpsa0n8k85f3xbi0mv34", "depends": ["Biobase", "FactoMineR", "GGally", "Kendall", "MASS", "data_table", "dplyr", "factoextra", "flexdashboard", "genefilter", "ggplot2", "ggpubr", "gtools", "htmltools", "knitr", "limma", "magrittr", "pheatmap", "plotly", "plyr", "purrr", "readr", "remotes", "rlang", "rmarkdown", "shiny", "shinydashboard", "styler", "tibble", "tidyr", "vsn"] }, "proteinProfiles": { "name": "proteinProfiles", "version": "1.48.0", "sha256": "0ylqnpg3drabx2ysv4larvwq93hcwzqk78g04iwbgzrmq87mcl0n", "depends": [] }, "psichomics": { "name": "psichomics", "version": "1.34.0", "sha256": "12g9x7jyx8pkbp0l47sqzvpshifaiqqbzsr1zp7d4m0iqjgm1wyh", "depends": ["AnnotationDbi", "AnnotationHub", "BiocFileCache", "DT", "R_utils", "Rcpp", "Rfast", "SummarizedExperiment", "XML", "cluster", "colourpicker", "data_table", "digest", "dplyr", "edgeR", "fastICA", "fastmatch", "ggplot2", "ggrepel", "highcharter", "htmltools", "httr", "jsonlite", "limma", "pairsD3", "plyr", "purrr", "recount", "reshape2", "shiny", "shinyBS", "shinyjs", "stringr", "survival", "xtable"] }, "ptairMS": { "name": "ptairMS", "version": "1.16.0", "sha256": "1rca11p9fklq6x69kd34rwans5m068k4nrafddl3171a972aikhb", "depends": ["Biobase", "DT", "Hmisc", "MSnbase", "Rcpp", "bit64", "chron", "data_table", "doParallel", "enviPat", "foreach", "ggplot2", "ggpubr", "gridExtra", "minpack_lm", "plotly", "rhdf5", "rlang", "scales", "shiny", "shinyscreenshot", "signal"] }, "puma": { "name": "puma", "version": "3.50.0", "sha256": "0kvhq7xvldg2s5ib51gbl6ji3xczgzl9rhixrrygxkrffrwjql8b", "depends": ["Biobase", "affy", "affyio", "mclust", "oligo", "oligoClasses"] }, "pvac": { "name": "pvac", "version": "1.56.0", "sha256": "03ny0gjx107w26l0hkd2n9gpkdni0y42f0iz87jfqpks0l3sfyk2", "depends": ["Biobase", "affy"] }, "pvca": { "name": "pvca", "version": "1.48.0", "sha256": "0phqz3rhns83p49zz1n1h72hi501gq9z98kz8hxc3rrcinbxmq2w", "depends": ["Biobase", "Matrix", "lme4", "vsn"] }, "pwalign": { "name": "pwalign", "version": "1.4.0", "sha256": "1v4iicyr37fb5whx8qrslqy7rvnydvvjb5dhf78vfq7q47497363", "depends": ["BiocGenerics", "Biostrings", "IRanges", "S4Vectors", "XVector"] }, "qPLEXanalyzer": { "name": "qPLEXanalyzer", "version": "1.26.0", "sha256": "1mjkbzdqb8ksnwsi3fm8nj2rf3zi8lpr02dl6igpk5hav26gmq2z", "depends": ["Biobase", "BiocGenerics", "Biostrings", "IRanges", "MSnbase", "RColorBrewer", "assertthat", "dplyr", "ggdendro", "ggplot2", "limma", "magrittr", "preprocessCore", "purrr", "readr", "rlang", "scales", "stringr", "tibble", "tidyr", "tidyselect"] }, "qckitfastq": { "name": "qckitfastq", "version": "1.24.0", "sha256": "16lcg42jclw24nk1k9bxy7vm3qj5vyqny99b0ixm0ilda6wkl1f7", "depends": ["RSeqAn", "Rcpp", "data_table", "dplyr", "ggplot2", "magrittr", "reshape2", "rlang", "seqTools", "zlibbioc"] }, "qcmetrics": { "name": "qcmetrics", "version": "1.46.0", "sha256": "0vqm62wsn3c8rk02dzlm6af0k238anrhhlj47qrkk28d8mchsjwc", "depends": ["Biobase", "S4Vectors", "knitr", "pander", "xtable"] }, "qmtools": { "name": "qmtools", "version": "1.12.0", "sha256": "1ipwy43w1cx208nrrg1kdnd7mnylrjq7zjyxgk616bsh7q65jzrv", "depends": ["MsCoreUtils", "SummarizedExperiment", "VIM", "ggplot2", "heatmaply", "igraph", "limma", "patchwork", "rlang", "scales"] }, "qpcrNorm": { "name": "qpcrNorm", "version": "1.66.0", "sha256": "0rlfswzkzwxmdfkyzg33ckfzwk9ylw7grjgsy4h3lca5nxf8xvq4", "depends": ["Biobase", "affy", "limma"] }, "qpgraph": { "name": "qpgraph", "version": "2.42.0", "sha256": "0p116qywrr4ngqkhc9darzqdii6saqs7yxn0pqadq52vivmilzqh", "depends": ["AnnotationDbi", "Biobase", "BiocParallel", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "Rgraphviz", "S4Vectors", "annotate", "graph", "mvtnorm", "qtl"] }, "qsea": { "name": "qsea", "version": "1.34.0", "sha256": "0alvx8kq3whi89nxgdk64gr1hndkdma4mhivvkm3v8l5v1cp9w98", "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicRanges", "HMMcopy", "IRanges", "Rsamtools", "S4Vectors", "gtools", "limma", "rtracklayer", "zoo"] }, "qsmooth": { "name": "qsmooth", "version": "1.24.0", "sha256": "07bisfk8mx6aiylnkx7c6appwir9hrqnd5pms6q2hy3fc7lwsq3q", "depends": ["Hmisc", "SummarizedExperiment", "sva"] }, "qsvaR": { "name": "qsvaR", "version": "1.12.0", "sha256": "0cksc2rkg8cqa6dj23p368xj9415dff3c3fn0fnf263b8aql6kcw", "depends": ["SummarizedExperiment", "dplyr", "ggplot2", "rlang", "sva"] }, "quantiseqr": { "name": "quantiseqr", "version": "1.16.0", "sha256": "0gw1cy8m71qykvwy4pa2bg20r4gbpwlki7sar9d7cg20x5nwz22s", "depends": ["Biobase", "MASS", "SummarizedExperiment", "ggplot2", "limSolve", "preprocessCore", "rlang", "tidyr"] }, "quantro": { "name": "quantro", "version": "1.42.0", "sha256": "18yixnla95ch595phf2dr7zpzg049bra8dhciawj0731rj158i73", "depends": ["Biobase", "RColorBrewer", "doParallel", "foreach", "ggplot2", "iterators", "minfi"] }, "quantsmooth": { "name": "quantsmooth", "version": "1.74.0", "sha256": "19y817s9k86q79hmnj05573wrybglp5qzsywasn1h6hgvdnrd97h", "depends": ["quantreg"] }, "qusage": { "name": "qusage", "version": "2.42.0", "sha256": "1jzfzsaw59iwb3k61ji9dpzl5bd4dfpmna8k0c359pv7c861310b", "depends": ["Biobase", "emmeans", "fftw", "limma", "nlme"] }, "qvalue": { "name": "qvalue", "version": "2.40.0", "sha256": "1ylmqdlsixwz3d31l6pwbifczadh98s5j7ff5gpps8k8wv8bbnlm", "depends": ["ggplot2", "reshape2"] }, "r3Cseq": { "name": "r3Cseq", "version": "1.54.0", "sha256": "1zs6plfb0wpjim5bv5q0cw2am69frlz2vlk424m7i3142d144w6v", "depends": ["Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "VGAM", "data_table", "qvalue", "rtracklayer", "sqldf"] }, "rBLAST": { "name": "rBLAST", "version": "1.4.0", "sha256": "14drh961jizyn0y0lp4xm2dcbxrp7z1xvv74fnlr3my60p3746aj", "depends": ["BiocFileCache", "Biostrings"] }, "rBiopaxParser": { "name": "rBiopaxParser", "version": "2.48.0", "sha256": "0ggabwpsrs0dwim47p18brhyi51zmxkrjdnvpz8hpkmy570jljf6", "depends": ["XML", "data_table"] }, "rCGH": { "name": "rCGH", "version": "1.38.0", "sha256": "10lwvrmcc1nw7ci0bb20id32xs0f2wkbyjmqsck7rfiwfyccvg6h", "depends": ["AnnotationDbi", "DNAcopy", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "TxDb_Hsapiens_UCSC_hg18_knownGene", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "aCGH", "affy", "ggplot2", "lattice", "limma", "mclust", "org_Hs_eg_db", "plyr", "shiny"] }, "rGADEM": { "name": "rGADEM", "version": "2.55.0", "sha256": "1fjqvkayam7xpvvbdlz6nafgsrw46vgmbkl96mfvm4szclrxzs8g", "depends": ["BSgenome", "Biostrings", "GenomicRanges", "IRanges", "seqLogo"] }, "rGREAT": { "name": "rGREAT", "version": "2.10.0", "sha256": "1fhgwkyx11300aqvm2rz2gwqk3lh0blpdcqg439wi7ql3m0q5k9k", "depends": ["AnnotationDbi", "DT", "GO_db", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "GetoptLong", "GlobalOptions", "IRanges", "RColorBrewer", "RCurl", "Rcpp", "S4Vectors", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "circlize", "digest", "doParallel", "foreach", "org_Hs_eg_db", "progress", "rjson", "shiny"] }, "rGenomeTracks": { "name": "rGenomeTracks", "version": "1.14.0", "sha256": "0j8p7k64djin5njrglw47j7ysfna7x5b45nchzrqk7zy20w5rdik", "depends": ["imager", "rGenomeTracksData", "reticulate"] }, "rRDP": { "name": "rRDP", "version": "1.42.0", "sha256": "0s3k0hh62dl6lcfqgi2hm0x7v62vwq345gd1w1rirfbajzv775ks", "depends": ["Biostrings", "rJava"] }, "rSWeeP": { "name": "rSWeeP", "version": "1.20.0", "sha256": "1a2wzy1r7ifr1bzrxrbymj8f7353w9vg5vsh2ym1cimj6c89pln5", "depends": ["Biostrings", "doParallel", "foreach", "stringi"] }, "rScudo": { "name": "rScudo", "version": "1.24.0", "sha256": "0agzx7fi36jwgklfz16rqzm9x9qmi5j5xz3hsh72lymzffmn5ca7", "depends": ["Biobase", "BiocGenerics", "S4Vectors", "SummarizedExperiment", "igraph", "stringr"] }, "rTRM": { "name": "rTRM", "version": "1.46.0", "sha256": "1865zcx5gs09ysd047skz93b5rjf7l6yy764ld48p9m59al0h7ln", "depends": ["AnnotationDbi", "DBI", "RSQLite", "igraph"] }, "rTRMui": { "name": "rTRMui", "version": "1.46.0", "sha256": "1n3cz9v85c7wlqjsyyw60z8ly4jr393wphg9pksz44z87p048ygq", "depends": ["MotifDb", "org_Hs_eg_db", "org_Mm_eg_db", "rTRM", "shiny"] }, "rWikiPathways": { "name": "rWikiPathways", "version": "1.28.0", "sha256": "1rhs7mmn3q50ndkcr37smxqs7x8aq9imrp1ri5k2rmi82bhc805f", "depends": ["RCurl", "XML", "data_table", "dplyr", "httr", "lubridate", "purrr", "readr", "rjson", "stringr", "tidyr"] }, "raer": { "name": "raer", "version": "1.6.0", "sha256": "0dldr24abrdd2cl98m84pg2ziz2lcwi8f2n4xdf94iamzymck358", "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "Rhtslib", "Rsamtools", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "cli", "rtracklayer"] }, "rain": { "name": "rain", "version": "1.42.0", "sha256": "1vrqyr3px62hx8rbzfs51vrr81g75r2c3gz0c98gbp8pbfs7csjl", "depends": ["gmp", "multtest"] }, "ramr": { "name": "ramr", "version": "1.16.0", "sha256": "0yh304barqgr4zc6kk6jrn2s3i0r1vqmfvci72315laanm4c8vd5", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rcpp", "S4Vectors", "data_table"] }, "ramwas": { "name": "ramwas", "version": "1.32.0", "sha256": "1zycxy3rdg8nqs1jw7pdlydj7mnbm7ik9zxqmrmd5fbh2rjkqdp9", "depends": ["BiocGenerics", "Biostrings", "GenomicAlignments", "KernSmooth", "Rsamtools", "biomaRt", "digest", "filematrix", "glmnet"] }, "randPack": { "name": "randPack", "version": "1.54.0", "sha256": "0n8zai797awci326j6ihx2x53y9ymyh7yj490ir1v03riifq3pmb", "depends": ["Biobase"] }, "randRotation": { "name": "randRotation", "version": "1.20.0", "sha256": "19qhhf12x8z8wrdwvph9p9fx2ivzkk72n2mr97chj5n83wsxgvb4", "depends": ["Rdpack"] }, "rawDiag": { "name": "rawDiag", "version": "1.4.0", "sha256": "1944mgb1vx3y1vljm04x8ar640jjnsbdxqr0awwsd0ci99qjqw6i", "depends": ["BiocManager", "BiocParallel", "dplyr", "ggplot2", "hexbin", "htmltools", "rawrr", "reshape2", "rlang", "scales", "shiny"] }, "rawrr": { "name": "rawrr", "version": "1.16.0", "sha256": "1g5d4mga7wb5ygj7dybz87sn88va3yigxy2hc1s8m5p9a1bl0vz6", "depends": [] }, "rbsurv": { "name": "rbsurv", "version": "2.66.0", "sha256": "19qygdn3yx7a5jk2adqchpgw2jgznccg0hkp0wina7b0g8912jx0", "depends": ["Biobase", "survival"] }, "rcellminer": { "name": "rcellminer", "version": "2.30.1", "sha256": "067y9k9376x9vdkxghi6baarsif9f80cww2z7vdj01w2sw8jpffx", "depends": ["Biobase", "ggplot2", "gplots", "rcellminerData", "shiny", "stringr"] }, "rebook": { "name": "rebook", "version": "1.18.0", "sha256": "0xizyqw28bhgmg7s4a6jm1627z4iv3rglqczzwcfad152inyyypr", "depends": ["BiocStyle", "CodeDepends", "dir_expiry", "filelock", "knitr", "rmarkdown"] }, "receptLoss": { "name": "receptLoss", "version": "1.20.0", "sha256": "1b6lfs7dmizyvl1x21rf2h07pc04x7ains30zn64p8xrg6cxkfr9", "depends": ["SummarizedExperiment", "dplyr", "ggplot2", "magrittr", "tidyr"] }, "reconsi": { "name": "reconsi", "version": "1.20.0", "sha256": "0w0wjv7l3jajlspvyrmngd5134bxfjvisjvmvbsl56l0ws7ib92c", "depends": ["Matrix", "ggplot2", "ks", "matrixStats", "phyloseq", "reshape2"] }, "recount": { "name": "recount", "version": "1.34.0", "sha256": "0bwdid17vxzpxshb33c0kxfyqamb8jxsfl5v4pmlyscdv4lp3fhg", "depends": ["BiocParallel", "GEOquery", "GenomeInfoDb", "GenomicRanges", "IRanges", "RCurl", "S4Vectors", "SummarizedExperiment", "derfinder", "downloader", "rentrez", "rtracklayer"] }, "recount3": { "name": "recount3", "version": "1.18.0", "sha256": "1rzrkbi8wy94d08akrg7vzpv6a1jlpv4wjh2x1dr2pnsyx8lfnkc", "depends": ["BiocFileCache", "GenomicRanges", "Matrix", "R_utils", "S4Vectors", "SummarizedExperiment", "data_table", "httr", "rtracklayer", "sessioninfo"] }, "recountmethylation": { "name": "recountmethylation", "version": "1.18.0", "sha256": "06g3ahvcc5q33ngpk92vk1y1pqlnyazyg49jhv27580jvap64jmk", "depends": ["BiocFileCache", "DelayedMatrixStats", "HDF5Array", "RCurl", "R_utils", "S4Vectors", "basilisk", "minfi", "reticulate", "rhdf5"] }, "recoup": { "name": "recoup", "version": "1.36.0", "sha256": "020kb22ka0xxf430zdc7jwhhhq0djxskmaaqcr7a83vn6zn1r8z7", "depends": ["BiocGenerics", "Biostrings", "ComplexHeatmap", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "RSQLite", "Rsamtools", "S4Vectors", "biomaRt", "circlize", "ggplot2", "httr", "rtracklayer", "stringr", "txdbmaker"] }, "regionReport": { "name": "regionReport", "version": "1.42.0", "sha256": "0ksqk3qnb0mv7rm5zli2n8gih3izd6crfwci8vv6vy7wmx1bgraz", "depends": ["BiocStyle", "DEFormats", "DESeq2", "GenomeInfoDb", "GenomicRanges", "RefManageR", "S4Vectors", "SummarizedExperiment", "derfinder", "knitr", "knitrBootstrap", "rmarkdown"] }, "regionalpcs": { "name": "regionalpcs", "version": "1.6.0", "sha256": "07c66bi8df6pl6biim16z108mv5zb5cr7xzifm41vbfj2cwyjkdp", "depends": ["GenomicRanges", "PCAtools", "dplyr", "tibble"] }, "regioneR": { "name": "regioneR", "version": "1.40.1", "sha256": "1w8s1vzb2zxswizdw4gj73r7bpxpma7jh6lxkv454k4b8i85h3xc", "depends": ["BSgenome", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "memoise", "rtracklayer"] }, "regioneReloaded": { "name": "regioneReloaded", "version": "1.10.0", "sha256": "0md9wyhnfcbh0l7nj75gj5wqbx58485f0n9pmcyj4v8hwwzf03z6", "depends": ["RColorBrewer", "Rtsne", "cluster", "ggplot2", "ggrepel", "regioneR", "reshape2", "scales", "umap"] }, "regsplice": { "name": "regsplice", "version": "1.34.1", "sha256": "0wavby4gyxrabzc6gfv0jnqygiiq1ccakypx848n514amqvrjj11", "depends": ["S4Vectors", "SummarizedExperiment", "edgeR", "glmnet", "limma", "pbapply"] }, "regutools": { "name": "regutools", "version": "1.20.0", "sha256": "0sq41fn8c8s2xyk18lws5j7aqq89vw9vvhnc5w4r10avzrjx32f7", "depends": ["AnnotationDbi", "AnnotationHub", "BiocFileCache", "Biostrings", "DBI", "GenomicRanges", "Gviz", "IRanges", "RCy3", "RSQLite", "S4Vectors"] }, "retrofit": { "name": "retrofit", "version": "1.8.0", "sha256": "1hs4kyq2fzr1918fc6dp2pfr44bcx32aw6l40nahsipcr8jsz44p", "depends": ["Rcpp"] }, "rexposome": { "name": "rexposome", "version": "1.30.0", "sha256": "15by861nxm5xdvq1lq214gff3a7flk2srrjywnwhll9h6n6m5r0g", "depends": ["Biobase", "FactoMineR", "Hmisc", "S4Vectors", "circlize", "corrplot", "ggplot2", "ggrepel", "ggridges", "glmnet", "gplots", "gridExtra", "gtools", "imputeLCMD", "lme4", "lsr", "mice", "pryr", "reshape2", "scales", "scatterplot3d", "stringr"] }, "rfPred": { "name": "rfPred", "version": "1.46.0", "sha256": "008f4jy5cz9a9i8xfmwnjiyd9yplj9p9701xnfl70c330wzbh9pl", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "data_table"] }, "rfaRm": { "name": "rfaRm", "version": "1.20.0", "sha256": "1ll7z7qdzqjj0ax7pw66w7f2kwhh2dpydqwvqmn5h08k90q04aa1", "depends": ["Biostrings", "IRanges", "S4Vectors", "data_table", "httr", "jsonlite", "magick", "rsvg", "rvest", "stringi", "xml2"] }, "rgoslin": { "name": "rgoslin", "version": "1.12.0", "sha256": "0h9dxy13jv7mm47429k383a9mr73chh5yfv6blzcs6d31wgy69kp", "depends": ["Rcpp", "dplyr"] }, "rgsepd": { "name": "rgsepd", "version": "1.40.0", "sha256": "10x3xir9dfk78vqll55aharar6bj0r5kc1lrvi441qhj4jyzmjjk", "depends": ["AnnotationDbi", "DESeq2", "GO_db", "SummarizedExperiment", "biomaRt", "goseq", "gplots", "org_Hs_eg_db"] }, "rhdf5": { "name": "rhdf5", "version": "2.52.1", "sha256": "1i5jf15blg4c36648m2m66y66hical16j05jvqsfh4b0rnmd94yr", "depends": ["Rhdf5lib", "rhdf5filters"] }, "rhdf5client": { "name": "rhdf5client", "version": "1.30.0", "sha256": "0s4826xj8k12d2dja93n35dip55653vp7h0rb4a7gw67hk6c9853", "depends": ["DelayedArray", "data_table", "httr", "rjson"] }, "rhdf5filters": { "name": "rhdf5filters", "version": "1.20.0", "sha256": "1dqpjv9zl00vxhvghnc54sic0z5z6d7jwlsybcf6qs002dkm9haz", "depends": ["Rhdf5lib"] }, "rhinotypeR": { "name": "rhinotypeR", "version": "1.2.0", "sha256": "0xp81bg6hw4bbdgb90ps5bin3qqvyn9b8r8nwj1wvvizg3sv70in", "depends": ["Biostrings"] }, "riboSeqR": { "name": "riboSeqR", "version": "1.42.0", "sha256": "01rm4xjyh3q3slzm9gs3xifglh038if095vfg335xl2cwhpf6n4d", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "abind", "baySeq", "seqLogo"] }, "ribor": { "name": "ribor", "version": "1.20.0", "sha256": "18rhzvc6jkvi17zc5g8k3mk9kyiqldnxlq2d5s5rmxhgwfh4cjmf", "depends": ["S4Vectors", "dplyr", "ggplot2", "hash", "rhdf5", "rlang", "tidyr", "yaml"] }, "ribosomeProfilingQC": { "name": "ribosomeProfilingQC", "version": "1.20.0", "sha256": "0zjp5xdhfi5c3kp8f449fdjp3f0pcqc9xk6f2r5dydh9x6k9n66k", "depends": ["AnnotationDbi", "BSgenome", "BiocGenerics", "Biostrings", "EDASeq", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "RUVSeq", "Rsamtools", "Rsubread", "S4Vectors", "XVector", "cluster", "ggExtra", "ggfittext", "ggplot2", "ggrepel", "motifStack", "rtracklayer", "scales", "txdbmaker"] }, "rifi": { "name": "rifi", "version": "1.12.0", "sha256": "1abcxjysgm0s6g1alr5qncqmnwvnxvbfk7n08gnlz9ifbvrcmp19", "depends": ["S4Vectors", "SummarizedExperiment", "car", "cowplot", "doMC", "dplyr", "egg", "foreach", "ggplot2", "nls2", "nnet", "reshape2", "rlang", "rtracklayer", "scales", "stringr", "tibble"] }, "rifiComparative": { "name": "rifiComparative", "version": "1.8.0", "sha256": "1dw8aspwzd21q3y45qjbyan9im0xjx0223hkqpsdl423lf4cz9qa", "depends": ["DTA", "LSD", "S4Vectors", "SummarizedExperiment", "cowplot", "devtools", "doMC", "dplyr", "egg", "foreach", "ggplot2", "ggrepel", "nnet", "reshape2", "rlang", "rtracklayer", "scales", "stringr", "tibble", "writexl"] }, "rigvf": { "name": "rigvf", "version": "1.0.2", "sha256": "0fijdnk3vggxnaay93ggqzl1csfkv7zjjvivhfpd62jd1k6sqx93", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "cachem", "dplyr", "httr2", "jsonlite", "memoise", "rjsoncons", "rlang", "tidyr", "whisker"] }, "rmelting": { "name": "rmelting", "version": "1.24.0", "sha256": "0vsv2ja601chzm7zhk71sv6m5j0lwg6lq5j4r2g8ir76zwgxspjh", "depends": ["Rdpack", "rJava"] }, "rmspc": { "name": "rmspc", "version": "1.14.0", "sha256": "0a4m34hda6f8q4nbd3b46pknyfpqd5pfpyz6yviicmdagb4v0jk7", "depends": ["BiocManager", "GenomicRanges", "processx", "rtracklayer", "stringr"] }, "rnaEditr": { "name": "rnaEditr", "version": "1.18.0", "sha256": "0vcyvd7vgc36qmk92si8s6s730j7zx8bsfq51r1i4sakq0w9mqa6", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "bumphunter", "corrplot", "logistf", "plyr", "survival"] }, "rnaseqcomp": { "name": "rnaseqcomp", "version": "1.38.0", "sha256": "0b2kzf2qc3m9w6j8fwgzjd27gdqbb3wdhn6fhk9z0ccygy0hpz84", "depends": ["RColorBrewer"] }, "roar": { "name": "roar", "version": "1.44.1", "sha256": "12a5b4rrsqxdsgxikpxsjqv13117743nxadmrw0xbdpiq1ai4kmp", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "rtracklayer"] }, "roastgsa": { "name": "roastgsa", "version": "1.6.0", "sha256": "0f47zmr2a598z1y9cx1ryp379gk6b6k0skaqva8fwkmxnkiisqm0", "depends": ["Biobase", "RColorBrewer", "ggplot2", "gplots", "limma"] }, "rols": { "name": "rols", "version": "3.4.0", "sha256": "1v6sp43j9ls4mxmfhzr3slq9kbhsnhwk7400i832yk1p7i0l9h4v", "depends": ["Biobase", "BiocGenerics", "httr2", "jsonlite"] }, "ropls": { "name": "ropls", "version": "1.40.0", "sha256": "04alj2md21bx2x3sx37gag08l9ax8kv2pj185a4h6010rj7jmkbv", "depends": ["Biobase", "MultiAssayExperiment", "MultiDataSet", "SummarizedExperiment", "ggplot2", "plotly"] }, "rprimer": { "name": "rprimer", "version": "1.12.0", "sha256": "0wc6k5vavw8sxbbv0jf4hfly23gigqw9kvhppi6fdkc9dnkrcs6q", "depends": ["Biostrings", "DT", "IRanges", "S4Vectors", "bslib", "ggplot2", "mathjaxr", "patchwork", "reshape2", "shiny", "shinyFeedback", "shinycssloaders"] }, "rpx": { "name": "rpx", "version": "2.16.0", "sha256": "0za17mjy5784hh5ypymldqc178piq7g7ddlc7bdzg8za3zm8y4i6", "depends": ["BiocFileCache", "RCurl", "curl", "jsonlite", "xml2"] }, "rqt": { "name": "rqt", "version": "1.34.0", "sha256": "068iz0xf4pxf9fj17264s0w5y3ch56nkmpym3hs69rdqjhkb1fd1", "depends": ["CompQuadForm", "Matrix", "RUnit", "SummarizedExperiment", "car", "glmnet", "metap", "pls", "ropls"] }, "rqubic": { "name": "rqubic", "version": "1.54.0", "sha256": "0lcsqwjc1kjrn7ng719fy274hkf0sm7l0srp110105d0rzhzjiqg", "depends": ["Biobase", "BiocGenerics", "biclust"] }, "rrvgo": { "name": "rrvgo", "version": "1.20.0", "sha256": "04zdd1jpvn4qx3m28llyzldr64y081ini9k5xfi7pzs1jmk18dal", "depends": ["AnnotationDbi", "GOSemSim", "GO_db", "ggplot2", "ggrepel", "pheatmap", "shiny", "tm", "treemap", "umap", "wordcloud"] }, "rsbml": { "name": "rsbml", "version": "2.66.0", "sha256": "02qfdiwamlw6nds2lir2936zgs2gsv1rsnsvmsn2ld39i1i4vbg0", "depends": ["BiocGenerics", "graph"] }, "rsemmed": { "name": "rsemmed", "version": "1.18.0", "sha256": "0nkiygdcgr547b22zpwf5nan9al3cm3zsplga93g60ncjpc1bwkr", "depends": ["dplyr", "igraph", "magrittr", "stringr"] }, "rtracklayer": { "name": "rtracklayer", "version": "1.68.0", "sha256": "07lj0frvqaw062y0d5h52abklyw2ydnk3311a6ykwhhp0mvdskd2", "depends": ["BiocGenerics", "BiocIO", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "XML", "XVector", "curl", "httr", "restfulr"] }, "runibic": { "name": "runibic", "version": "1.30.0", "sha256": "18irwzjdvbswsdvwafpg8f265yywlavznwmv16h11xs4ydwy0pc0", "depends": ["Rcpp", "SummarizedExperiment", "biclust", "testthat"] }, "sRACIPE": { "name": "sRACIPE", "version": "2.0.1", "sha256": "0hbsj4q6shqykzapasa5zagfascrw5kkzkljhzl0g0kax6biynvm", "depends": ["BiocGenerics", "MASS", "RColorBrewer", "Rcpp", "S4Vectors", "SummarizedExperiment", "doFuture", "doRNG", "foreach", "future", "ggplot2", "gplots", "gridExtra", "htmlwidgets", "reshape2", "umap", "visNetwork"] }, "sSNAPPY": { "name": "sSNAPPY", "version": "1.12.0", "sha256": "0xb0biy2ni5g1hvvvgpn9nawwhk7dzj8nsdy451qji0g4nxkm60y", "depends": ["SummarizedExperiment", "dplyr", "edgeR", "ggforce", "ggplot2", "ggraph", "graphite", "gtools", "igraph", "magrittr", "org_Hs_eg_db", "pheatmap", "reshape2", "rlang", "stringr", "tibble", "tidyr"] }, "sSeq": { "name": "sSeq", "version": "1.46.0", "sha256": "0308pqsbaqa0a5hamhnykq4423sgkmrmz1j78sbh63m7nvm3jr1n", "depends": ["RColorBrewer", "caTools"] }, "safe": { "name": "safe", "version": "3.48.0", "sha256": "05lgqw0c8rm9mrhm2hbr10paqvzibgrv3fg6zmp1jsl7ic787y5p", "depends": ["AnnotationDbi", "Biobase", "SparseM"] }, "sagenhaft": { "name": "sagenhaft", "version": "1.78.0", "sha256": "188qgkmw9j9whrm1lfgcdyjayiz3xm44ajh85hxw0crhj85sahg5", "depends": ["SparseM"] }, "sampleClassifier": { "name": "sampleClassifier", "version": "1.32.0", "sha256": "18cmgpwwd54mkkpg13wjznbk71lp0bz1p5ics9mhxiq6vfw8i62l", "depends": ["MGFM", "MGFR", "annotate", "e1071", "ggplot2"] }, "sangeranalyseR": { "name": "sangeranalyseR", "version": "1.18.0", "sha256": "1dy2n7d430b19lkl8104hmp9k3azl92j7n41h4a74155n0zsfy5v", "depends": ["BiocStyle", "Biostrings", "DECIPHER", "DT", "ape", "data_table", "excelR", "ggdendro", "gridExtra", "knitr", "logger", "openxlsx", "plotly", "pwalign", "reshape2", "rmarkdown", "sangerseqR", "seqinr", "shiny", "shinyWidgets", "shinycssloaders", "shinydashboard", "shinyjs", "stringr", "zeallot"] }, "sangerseqR": { "name": "sangerseqR", "version": "1.44.0", "sha256": "116adlm2a82c5jsljpicsfq34yyks9jcnmn9qjbfb4s8arvq14fw", "depends": ["Biostrings", "pwalign", "shiny", "stringr"] }, "sarks": { "name": "sarks", "version": "1.20.0", "sha256": "1b0szlwp7p5rcyvi4ndqxa0cdn5g89rxnfya6fg5arc93bdbgkq5", "depends": ["Biostrings", "IRanges", "binom", "cluster", "rJava"] }, "saseR": { "name": "saseR", "version": "1.4.0", "sha256": "0dndj7r195qwd0y9lm25wdk94b15gpimsck6i0v58nnfjldjgyds", "depends": ["ASpli", "BiocGenerics", "BiocParallel", "DESeq2", "DEXSeq", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "MASS", "MatrixGenerics", "PRROC", "S4Vectors", "SummarizedExperiment", "data_table", "dplyr", "edgeR", "igraph", "knitr", "limma", "pracma", "precrec", "rrcov"] }, "satuRn": { "name": "satuRn", "version": "1.16.0", "sha256": "1vimbg778fph2rc95jq0z4ynz38d4cz9nj50iwrxz7j4arzndvg9", "depends": ["BiocParallel", "Matrix", "SummarizedExperiment", "boot", "ggplot2", "limma", "locfdr", "pbapply"] }, "scAnnotatR": { "name": "scAnnotatR", "version": "1.14.0", "sha256": "1p3ws64rj4mraha4c9gw930g7r75n3g3r3m464l41cnli1w39fwi", "depends": ["AnnotationHub", "ROCR", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "ape", "caret", "data_tree", "dplyr", "e1071", "ggplot2", "kernlab", "pROC"] }, "scBFA": { "name": "scBFA", "version": "1.22.0", "sha256": "08gy0rnpdgif942p5kw8rhgbfjfbz3c8j3ji7mhhlgr8dnqhbqfl", "depends": ["DESeq2", "MASS", "Matrix", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "copula", "ggplot2", "zinbwave"] }, "scBubbletree": { "name": "scBubbletree", "version": "1.10.0", "sha256": "0wjafjxmv2hlmdc7hr381g3z2732429ixhlifj8gcz27j6m9g77g", "depends": ["BiocParallel", "Seurat", "ape", "dplyr", "ggplot2", "ggtree", "patchwork", "proxy", "reshape2", "scales"] }, "scCB2": { "name": "scCB2", "version": "1.18.0", "sha256": "11vk83l923bnry1b18g7hap3k5rfi6ww46z556d8vxymjkcd4363", "depends": ["DropletUtils", "Matrix", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "doParallel", "edgeR", "foreach", "iterators", "rhdf5"] }, "scClassify": { "name": "scClassify", "version": "1.20.0", "sha256": "1j1z715xr1sxb3vg528kqnch2vqnirl7mm4k8r2qiacq31jx10kg", "depends": ["BiocParallel", "Cepo", "Matrix", "S4Vectors", "cluster", "diptest", "ggplot2", "ggraph", "hopach", "igraph", "limma", "mgcv", "minpack_lm", "mixtools", "proxy", "proxyC", "statmod"] }, "scDD": { "name": "scDD", "version": "1.32.0", "sha256": "19kz0ivv9qypq7jg33rds5rcjr1mmqd19j3fsj842c5h3bydssph", "depends": ["BiocParallel", "EBSeq", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "arm", "fields", "ggplot2", "mclust", "outliers", "scran"] }, "scDDboost": { "name": "scDDboost", "version": "1.10.0", "sha256": "1rxwm3l6mk0sgg478dbhjpd8dvp6nr934ml8k1wb651a1hz2zqcl", "depends": ["BH", "BiocParallel", "EBSeq", "Oscope", "Rcpp", "RcppEigen", "SingleCellExperiment", "SummarizedExperiment", "cluster", "ggplot2", "mclust"] }, "scDataviz": { "name": "scDataviz", "version": "1.18.0", "sha256": "0d8dvnan7d1rwg18f32hajqcpix88wx6j2p0wx4cn3z584jn32ih", "depends": ["MASS", "RColorBrewer", "S4Vectors", "Seurat", "SingleCellExperiment", "corrplot", "flowCore", "ggplot2", "ggrepel", "matrixStats", "reshape2", "scales", "umap"] }, "scDblFinder": { "name": "scDblFinder", "version": "1.22.0", "sha256": "08nn6a3kina6l5b6m9q7jwkwzjw276k85ypsjhf04yi5nxxggy8s", "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "DelayedArray", "GenomeInfoDb", "GenomicRanges", "IRanges", "MASS", "Matrix", "Rsamtools", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "bluster", "igraph", "rtracklayer", "scater", "scran", "scuttle", "xgboost"] }, "scDesign3": { "name": "scDesign3", "version": "1.6.0", "sha256": "18b2xdhm4fgxj6f9kzp37v9xfa8p9yij88nar6gyvn6p04a8ar5f", "depends": ["BiocParallel", "Matrix", "SingleCellExperiment", "SummarizedExperiment", "coop", "dplyr", "gamlss", "gamlss_dist", "ggplot2", "irlba", "matrixStats", "mclust", "mgcv", "mvtnorm", "pbmcapply", "rvinecopulib", "sparseMVN", "tibble", "umap", "viridis"] }, "scDiagnostics": { "name": "scDiagnostics", "version": "1.2.0", "sha256": "1b974j1a6670ln6qbl9p07cic6g0am1kpym539g7vrwlsg21sn1n", "depends": ["SingleCellExperiment", "SummarizedExperiment", "bluster", "cramer", "ggplot2", "ggridges", "isotree", "patchwork", "ranger", "rlang", "speedglm", "transport"] }, "scDotPlot": { "name": "scDotPlot", "version": "1.2.1", "sha256": "1zdfa1pqccx88m4j3dkdqbl4lq7w1w1cgfajvh11005ywmd39g12", "depends": ["BiocGenerics", "Seurat", "SingleCellExperiment", "aplot", "cli", "dplyr", "ggplot2", "ggsci", "ggtree", "magrittr", "purrr", "rlang", "scales", "scater", "stringr", "tibble", "tidyr"] }, "scFeatureFilter": { "name": "scFeatureFilter", "version": "1.28.0", "sha256": "0kpjk6ylm9kxyaynjkd61y3gdgkh7415liw2azmymm641k3h1h7j", "depends": ["dplyr", "ggplot2", "magrittr", "rlang", "tibble"] }, "scFeatures": { "name": "scFeatures", "version": "1.8.0", "sha256": "0srvd9jayyy3793jmm7pcq70m4mhvdc9qhsszbnnl2qcd33wsnkv", "depends": ["AUCell", "BiocParallel", "DT", "DelayedArray", "DelayedMatrixStats", "EnsDb_Hsapiens_v79", "EnsDb_Mmusculus_v79", "GSVA", "MatrixGenerics", "Seurat", "SingleCellSignalR", "ape", "cli", "dplyr", "ensembldb", "glue", "gtools", "msigdbr", "proxyC", "reshape2", "rmarkdown", "spatstat_explore", "spatstat_geom", "tidyr"] }, "scGPS": { "name": "scGPS", "version": "1.22.0", "sha256": "0j5b6jq3qafhsx240sinmcf8hrg7290x3l8mfcibjpq3mkrhv0h9", "depends": ["DESeq2", "Rcpp", "RcppArmadillo", "RcppParallel", "SingleCellExperiment", "SummarizedExperiment", "caret", "dplyr", "dynamicTreeCut", "fastcluster", "ggplot2", "glmnet", "locfit"] }, "scHOT": { "name": "scHOT", "version": "1.20.1", "sha256": "0x1f7rvsrxs85mgf251qfj204ly6ibhvw0micvv65pf20f7430nk", "depends": ["BiocParallel", "IRanges", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "ggforce", "ggplot2", "igraph", "reshape"] }, "scHiCcompare": { "name": "scHiCcompare", "version": "1.0.0", "sha256": "1cyhhacrvicz3870rpr4l4v0cpjfhphnqgiiqwxxl2qacqq45wr0", "depends": ["BiocParallel", "HiCcompare", "data_table", "dplyr", "ggplot2", "gtools", "lattice", "mclust", "mice", "miceadds", "ranger", "rlang", "rstatix", "tidyr"] }, "scMET": { "name": "scMET", "version": "1.10.0", "sha256": "1jrr9d5si7wgy07sg0z9qdr1zy9wkc2qks02viwfnwdz92kp9x6m", "depends": ["BH", "BiocStyle", "MASS", "Matrix", "Rcpp", "RcppEigen", "RcppParallel", "S4Vectors", "SingleCellExperiment", "StanHeaders", "SummarizedExperiment", "VGAM", "assertthat", "coda", "cowplot", "data_table", "dplyr", "ggplot2", "logitnorm", "matrixStats", "rstan", "rstantools", "viridis"] }, "scMerge": { "name": "scMerge", "version": "1.24.0", "sha256": "1j5jm3gxkaymzr1karwx2ym5q62xxvfwixgw15yvnbays3v0kj5k", "depends": ["BiocNeighbors", "BiocParallel", "BiocSingular", "DelayedArray", "DelayedMatrixStats", "M3Drop", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "batchelor", "cluster", "cvTools", "distr", "igraph", "proxyC", "ruv", "scater", "scran"] }, "scMitoMut": { "name": "scMitoMut", "version": "1.4.0", "sha256": "1fhaf1ayy4b5z17jjbqj5yq0n1a06553cc5jklr7yynchqdl91a5", "depends": ["RColorBrewer", "Rcpp", "RcppArmadillo", "data_table", "ggplot2", "magrittr", "pheatmap", "plyr", "readr", "rhdf5", "stringr"] }, "scMultiSim": { "name": "scMultiSim", "version": "1.4.0", "sha256": "16vz69c55dmpcf4c38cv6j62mil8cpfym9714mg3hjq9alva5k2z", "depends": ["BiocParallel", "KernelKnn", "MASS", "Rtsne", "SummarizedExperiment", "ape", "assertthat", "crayon", "dplyr", "foreach", "ggplot2", "gplots", "igraph", "markdown", "matrixStats", "phytools", "rlang", "zeallot"] }, "scPCA": { "name": "scPCA", "version": "1.22.0", "sha256": "095bymrqx8fxl4pjcd2sj81j7lrggnaqzng5zkj61skcs0nf34kk", "depends": ["BiocParallel", "DelayedArray", "Matrix", "MatrixGenerics", "RSpectra", "Rdpack", "ScaledMatrix", "assertthat", "cluster", "coop", "dplyr", "elasticnet", "kernlab", "matrixStats", "origami", "purrr", "sparsepca", "stringr", "tibble"] }, "scPipe": { "name": "scPipe", "version": "2.8.0", "sha256": "13vqxd1p5pqbbbbcx9p5b4q21bs34sb31n9zbx1illrnwz5v484d", "depends": ["AnnotationDbi", "BiocGenerics", "Biostrings", "DropletUtils", "GGally", "GenomicAlignments", "GenomicRanges", "IRanges", "MASS", "Matrix", "MultiAssayExperiment", "Rcpp", "Rhtslib", "Rsamtools", "Rsubread", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "basilisk", "biomaRt", "data_table", "dplyr", "flexmix", "ggplot2", "glue", "hash", "magrittr", "mclust", "org_Hs_eg_db", "org_Mm_eg_db", "purrr", "reshape", "reticulate", "rlang", "robustbase", "rtracklayer", "scales", "stringr", "testthat", "tibble", "tidyr", "vctrs"] }, "scQTLtools": { "name": "scQTLtools", "version": "1.0.3", "sha256": "0k1ps1l56a7ybk28py515c39a9b798ysh7c47zj3w6fqncc6gpl7", "depends": ["DESeq2", "GOSemSim", "Matrix", "SeuratObject", "SingleCellExperiment", "SummarizedExperiment", "VGAM", "biomaRt", "dplyr", "gamlss", "ggplot2", "limma", "magrittr", "patchwork", "progress", "stringr"] }, "scRNAseqApp": { "name": "scRNAseqApp", "version": "1.8.0", "sha256": "0q6vlrxk5v463mvddcz42m747cv2z7kvzl3zbbx5823s1rk5syx4", "depends": ["ComplexHeatmap", "DBI", "DT", "GenomeInfoDb", "GenomicRanges", "IRanges", "Matrix", "RColorBrewer", "RSQLite", "RefManageR", "Rsamtools", "S4Vectors", "Seurat", "SeuratObject", "SingleCellExperiment", "bibtex", "bslib", "circlize", "colourpicker", "data_table", "fs", "ggdendro", "ggforce", "ggplot2", "ggrepel", "ggridges", "gridExtra", "htmltools", "jsonlite", "magrittr", "patchwork", "plotly", "rhdf5", "rtracklayer", "scales", "scrypt", "shiny", "shinyhelper", "shinymanager", "slingshot", "sortable", "xfun", "xml2"] }, "scReClassify": { "name": "scReClassify", "version": "1.14.0", "sha256": "13xbcby3pc7f38af42sdq2nv57kr7sfzxprk70i8fs9jkajbxk5w", "depends": ["SingleCellExperiment", "SummarizedExperiment", "e1071", "randomForest"] }, "scRecover": { "name": "scRecover", "version": "1.24.0", "sha256": "1g1yj2w3v5f5smh17qm7wk0r7cnx020iiya0dbvx6ziyhy6c5xyj", "depends": ["BiocParallel", "MASS", "Matrix", "SAVER", "bbmle", "doParallel", "foreach", "gamlss", "kernlab", "penalized", "preseqR", "pscl", "rsvd"] }, "scRepertoire": { "name": "scRepertoire", "version": "2.4.0", "sha256": "1lywcwh7zbjnfad2lxma5xxq33ah0kai65nxahls0lfk0j4xibyw", "depends": ["Rcpp", "S4Vectors", "SeuratObject", "SingleCellExperiment", "SummarizedExperiment", "VGAM", "assertthat", "cubature", "dplyr", "evmix", "ggalluvial", "ggdendro", "ggplot2", "ggraph", "iNEXT", "igraph", "lifecycle", "plyr", "purrr", "quantreg", "reshape2", "rjson", "rlang", "stringdist", "stringr", "tidygraph", "truncdist"] }, "scShapes": { "name": "scShapes", "version": "1.14.0", "sha256": "1m3kxysv96ir16d8rsnwsfprfq96r1iyh2ahl6c5jdn50zwycjv4", "depends": ["BiocParallel", "MASS", "Matrix", "VGAM", "dgof", "emdbook", "magrittr", "pscl"] }, "scTGIF": { "name": "scTGIF", "version": "1.22.0", "sha256": "0q4nz5vgawvlacgxai2p6v28qzh5766ypvd2wp348k2gzjdj91sv", "depends": ["Biobase", "BiocStyle", "GSEABase", "RColorBrewer", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "igraph", "knitr", "msigdbr", "nnTensor", "plotly", "rmarkdown", "scales", "schex", "tagcloud", "tibble"] }, "scTHI": { "name": "scTHI", "version": "1.20.0", "sha256": "0b6vg445cags0vbxlbcqb5zchc6v2v2mf5jz70pxwjh68p3rwazn", "depends": ["BiocParallel", "Rtsne"] }, "scTensor": { "name": "scTensor", "version": "2.18.2", "sha256": "1410amdbbzw8c4gn5lkidaxqrm2wlw564a5rgrfln55sn6w0k9lg", "depends": ["AnnotationDbi", "AnnotationHub", "BiocManager", "BiocStyle", "Category", "DOSE", "GOstats", "MeSHDbi", "RSQLite", "ReactomePA", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "abind", "ccTensor", "checkmate", "crayon", "ggplot2", "heatmaply", "igraph", "knitr", "meshr", "nnTensor", "outliers", "plotly", "plotrix", "rTensor", "reactome_db", "rmarkdown", "schex", "tagcloud", "visNetwork"] }, "scTreeViz": { "name": "scTreeViz", "version": "1.14.1", "sha256": "1r62cx7isp1psxa2di79fx19d0sqhaz24mkj218mavf9j9v7qf7n", "depends": ["Matrix", "Rtsne", "S4Vectors", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "clustree", "data_table", "digest", "epivizr", "epivizrData", "epivizrServer", "ggplot2", "ggraph", "httr", "igraph", "scater", "scran", "sys"] }, "scanMiR": { "name": "scanMiR", "version": "1.14.0", "sha256": "1s3k3hb4x666xczzilbb39nfir0z5sb30q0im0cfxibcjbgm5sps", "depends": ["BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "cowplot", "data_table", "ggplot2", "pwalign", "seqLogo", "stringi"] }, "scanMiRApp": { "name": "scanMiRApp", "version": "1.14.0", "sha256": "0xswhxnyigmm50wz4jdp0a1w8sjb6hyz7zgs30rcdiqk0fw8lfsz", "depends": ["AnnotationDbi", "AnnotationFilter", "AnnotationHub", "BiocParallel", "Biostrings", "DT", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "S4Vectors", "data_table", "digest", "ensembldb", "fst", "ggplot2", "htmlwidgets", "plotly", "rintrojs", "rtracklayer", "scanMiR", "scanMiRData", "shiny", "shinycssloaders", "shinydashboard", "shinyjqui", "txdbmaker", "waiter"] }, "scater": { "name": "scater", "version": "1.36.0", "sha256": "12rbjzwbxs78z62p6lfpgb241ah3c5ks6l1vgfz8ysfv5x7j3hpv", "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "DelayedArray", "Matrix", "MatrixGenerics", "RColorBrewer", "RcppML", "Rtsne", "S4Vectors", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "beachmat", "ggbeeswarm", "ggplot2", "ggrastr", "ggrepel", "pheatmap", "rlang", "scuttle", "uwot", "viridis"] }, "scatterHatch": { "name": "scatterHatch", "version": "1.14.0", "sha256": "0r15vzncmrw52wc8lrv17c4g9sgs2923j3xxafn15k5xiyl3hlk3", "depends": ["ggplot2", "plyr", "spatstat_geom"] }, "sccomp": { "name": "sccomp", "version": "2.0.0", "sha256": "0iy9rjzbdvabmcj09lp3jp495kqxi82513j8f2yfs2icqk41ilzd", "depends": ["SingleCellExperiment", "boot", "crayon", "dplyr", "forcats", "ggplot2", "ggrepel", "glue", "instantiate", "lifecycle", "magrittr", "patchwork", "purrr", "readr", "rlang", "scales", "stringr", "tibble", "tidyr", "tidyselect"] }, "scde": { "name": "scde", "version": "2.36.0", "sha256": "09i6bzwasbv83d7hgq7ld4dn8pmipxlgpvzl69hc2cblzl18ffd8", "depends": ["BiocParallel", "Cairo", "MASS", "RColorBrewer", "RMTstat", "Rcpp", "RcppArmadillo", "Rook", "edgeR", "extRemes", "flexmix", "mgcv", "nnet", "pcaMethods", "quantreg", "rjson"] }, "scds": { "name": "scds", "version": "1.24.0", "sha256": "10ylhdxgz6rj4di1xwayprxwfmm8q1w3z98f2012yd89jkqvnykx", "depends": ["Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "dplyr", "pROC", "xgboost"] }, "schex": { "name": "schex", "version": "1.22.0", "sha256": "1pay6f3vl5yl0xm70b4g05ck8yvh4p389rfabjn5drl0b43nb37q", "depends": ["SingleCellExperiment", "cluster", "concaveman", "dplyr", "entropy", "ggforce", "ggplot2", "hexbin", "rlang"] }, "scider": { "name": "scider", "version": "1.6.0", "sha256": "08bp6yjxdkia0ykgyyapra02rz2qgq5z66pkg2pjppsis1k626cn", "depends": ["S4Vectors", "SpatialExperiment", "SummarizedExperiment", "ggplot2", "igraph", "isoband", "janitor", "knitr", "lwgeom", "pheatmap", "plotly", "rlang", "sf", "shiny", "spatstat_explore", "spatstat_geom"] }, "scifer": { "name": "scifer", "version": "1.10.0", "sha256": "0c2qkqn36wd15a3gp9l7kn2g6nz4hkapwvwvv67gk1fp5kz36dyd", "depends": ["Biostrings", "DECIPHER", "basilisk", "basilisk_utils", "data_table", "dplyr", "flowCore", "ggplot2", "gridExtra", "here", "kableExtra", "knitr", "plyr", "reticulate", "rlang", "rmarkdown", "sangerseqR", "scales", "stringr", "tibble"] }, "scmap": { "name": "scmap", "version": "1.30.0", "sha256": "091n1703ngh50qkv1dynxszs0mqdawz8mm0n9mhsiiw38z4cg63d", "depends": ["Biobase", "BiocGenerics", "Rcpp", "RcppArmadillo", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "dplyr", "e1071", "ggplot2", "googleVis", "matrixStats", "proxy", "randomForest", "reshape2"] }, "scmeth": { "name": "scmeth", "version": "1.28.0", "sha256": "1zi5pa73qy5i0v6xma8la9l9hdh31yg6x1ha5m6i46g45wsh9bdc", "depends": ["AnnotationHub", "BSgenome", "Biostrings", "DT", "DelayedArray", "GenomeInfoDb", "GenomicRanges", "HDF5Array", "SummarizedExperiment", "annotatr", "bsseq", "knitr", "reshape2", "rmarkdown"] }, "scone": { "name": "scone", "version": "1.32.1", "sha256": "02naiyncpvz1x3rwcr8zniwfag53if70jyinm6pfyvhv5h027g06", "depends": ["BiocParallel", "DelayedMatrixStats", "MatrixGenerics", "RColorBrewer", "RUVSeq", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "aroma_light", "boot", "class", "cluster", "compositions", "diptest", "edgeR", "fpc", "gplots", "hexbin", "limma", "matrixStats", "mixtools", "rARPACK", "rhdf5", "sparseMatrixStats"] }, "scoreInvHap": { "name": "scoreInvHap", "version": "1.30.0", "sha256": "17mckzfw5aqyw2v1j02rm67d4dic9zdqiq9yz5nadmj4wvvg1259", "depends": ["BiocParallel", "Biostrings", "GenomicRanges", "SummarizedExperiment", "VariantAnnotation", "snpStats"] }, "scoup": { "name": "scoup", "version": "1.2.0", "sha256": "0231zmyp8iqmcmgrbhlqmfq6i55lhdg0wy6zgsq49l159ac043gs", "depends": ["Biostrings", "Matrix"] }, "scp": { "name": "scp", "version": "1.18.0", "sha256": "0gljfvpn6rajppgk4jdnzdh90ghiasajkzyk1rxk61awp8wmlswl", "depends": ["IHW", "MsCoreUtils", "MultiAssayExperiment", "QFeatures", "RColorBrewer", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "ggrepel", "matrixStats", "metapod", "nipals"] }, "scran": { "name": "scran", "version": "1.36.0", "sha256": "0y2hcxri6w1jqg3hcmn5y3ys59q7nxxd0ynv1d66fwgblwbi856x", "depends": ["BH", "BiocGenerics", "BiocParallel", "BiocSingular", "DelayedArray", "Matrix", "MatrixGenerics", "Rcpp", "S4Arrays", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "beachmat", "bluster", "dqrng", "edgeR", "igraph", "limma", "metapod", "scuttle", "statmod"] }, "scrapper": { "name": "scrapper", "version": "1.2.1", "sha256": "186srh8lkr7xfy2alxgqd2gg5liqwxsdrnc88wcvh2iv71gqybv4", "depends": ["BiocNeighbors", "DelayedArray", "Rcpp", "Rigraphlib", "assorthead", "beachmat"] }, "screenCounter": { "name": "screenCounter", "version": "1.8.0", "sha256": "0qiqjn2iiwrabfvg92czx5c15fv6pharywg4mdbf989k0k4ivq8c", "depends": ["BiocParallel", "Rcpp", "S4Vectors", "SummarizedExperiment"] }, "scruff": { "name": "scruff", "version": "1.26.0", "sha256": "0pqpz83lc9djjqnjanrg18mcbmgv979s15daz6ndb78l83k8v24r", "depends": ["AnnotationDbi", "BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Rsamtools", "Rsubread", "S4Vectors", "ShortRead", "SingleCellExperiment", "SummarizedExperiment", "data_table", "ggbio", "ggplot2", "ggthemes", "parallelly", "plyr", "rtracklayer", "scales", "stringdist", "txdbmaker"] }, "scry": { "name": "scry", "version": "1.20.0", "sha256": "07v96b4ydzil9d80gjpifs8dvd92273g32pp3pmzi386f569bxdw", "depends": ["BiocSingular", "DelayedArray", "Matrix", "SingleCellExperiment", "SummarizedExperiment", "glmpca"] }, "scuttle": { "name": "scuttle", "version": "1.18.0", "sha256": "0y3fa8bvjpzv45z2kmxc1ii46yw2rrkam229na3107l1a1wg80iq", "depends": ["BiocGenerics", "BiocParallel", "DelayedArray", "GenomicRanges", "Matrix", "MatrixGenerics", "Rcpp", "S4Arrays", "S4Vectors", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "beachmat"] }, "scviR": { "name": "scviR", "version": "1.8.0", "sha256": "1m0p4l8s8bgsbmcd9qb0shax5fdhlk7j2g31vms8asypah0m9am0", "depends": ["BiocFileCache", "MatrixGenerics", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "basilisk", "limma", "pheatmap", "reticulate", "scater", "shiny"] }, "seahtrue": { "name": "seahtrue", "version": "1.2.0", "sha256": "12klglc3sjp9qpkcrd7lhpk17f1fbsci5f8a89cnfp4rwmbqw7qh", "depends": ["RColorBrewer", "cli", "colorspace", "dplyr", "forcats", "ggplot2", "ggridges", "glue", "janitor", "logger", "lubridate", "purrr", "readr", "readxl", "rlang", "scales", "stringr", "tibble", "tidyr", "tidyxl", "validate"] }, "sechm": { "name": "sechm", "version": "1.16.0", "sha256": "0h1qc5qp1wv6qs9dy9wjs8xjdsqv933wxmpg71l80jwahixy3izp", "depends": ["ComplexHeatmap", "S4Vectors", "SummarizedExperiment", "circlize", "matrixStats", "randomcoloR", "seriation"] }, "segmentSeq": { "name": "segmentSeq", "version": "2.42.0", "sha256": "0smb0ch4ffj41gfr54wlk4lbxrdiywckjbb468x4ybgg4fd66my2", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "ShortRead", "abind", "baySeq"] }, "segmenter": { "name": "segmenter", "version": "1.14.0", "sha256": "0c59kgpgl60ks7z24a759i5yi8aj8vqkkyzkw2cr5a0hb8708y5j", "depends": ["ChIPseeker", "ComplexHeatmap", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "bamsignals", "chromhmmData"] }, "selectKSigs": { "name": "selectKSigs", "version": "1.20.0", "sha256": "0cnif7xvljzl83v7k6ky827kpk5kd3r8lzz78iwrinp2mw1gpp48", "depends": ["HiLDA", "Rcpp", "gtools", "magrittr"] }, "semisup": { "name": "semisup", "version": "1.32.0", "sha256": "0rjzk4zmvckxbmib7c094jkcs4ai3sj2i20cwqqig1hc6h95b6r9", "depends": ["VGAM"] }, "seq_hotSPOT": { "name": "seq.hotSPOT", "version": "1.8.0", "sha256": "0lsd109g423bp3fgw5fkvxdvgqz7a8iljac2qjny1hxx9spvyygb", "depends": ["R_utils", "hash"] }, "seq2pathway": { "name": "seq2pathway", "version": "1.40.0", "sha256": "1js23facw3z31fn4g8xrnxsvwfj4ij1spancl243wwnpdspw2vwy", "depends": ["GSA", "GenomicRanges", "WGCNA", "biomaRt", "nnet", "seq2pathway_data"] }, "seqArchR": { "name": "seqArchR", "version": "1.12.0", "sha256": "05i8ln6dbq46v4gnajmrfrnsi2y7mw22dzsmcbc6zni64c2r0186", "depends": ["BiocParallel", "Biostrings", "MASS", "Matrix", "cli", "cluster", "cvTools", "fpc", "ggplot2", "ggseqlogo", "matrixStats", "prettyunits", "reshape2", "reticulate"] }, "seqArchRplus": { "name": "seqArchRplus", "version": "1.8.0", "sha256": "17pby4jz6422ndfkxzq19r7js01ai2mp4m6jn1dj622a16gvgkp4", "depends": ["BSgenome", "BiocParallel", "Biostrings", "ChIPseeker", "GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "cli", "clusterProfiler", "cowplot", "factoextra", "ggimage", "ggplot2", "gridExtra", "heatmaps", "magick", "scales", "seqArchR", "seqPattern"] }, "seqCAT": { "name": "seqCAT", "version": "1.30.0", "sha256": "0v5cq5zlz7i6rq2d4s4sjz0wi508i9i6v93kkzq998mcc1ycd7y7", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "dplyr", "ggplot2", "rlang", "rtracklayer", "scales", "tidyr"] }, "seqLogo": { "name": "seqLogo", "version": "1.74.0", "sha256": "0sahhfdwzj976jghxy9chm7pdyksb1ncncfj70c1asrmd1q6if6h", "depends": [] }, "seqPattern": { "name": "seqPattern", "version": "1.40.0", "sha256": "1sjjvp87p0l9kzj27w3bfsp0ms1jqgw2b1isay9l21lkxc1v8y7x", "depends": ["Biostrings", "GenomicRanges", "IRanges", "KernSmooth", "plotrix"] }, "seqTools": { "name": "seqTools", "version": "1.42.0", "sha256": "0g9308wmrz9mkf8r1vg8pbz7z2bpcqd6invn30aka18r8kwcim7s", "depends": ["zlibbioc"] }, "seqcombo": { "name": "seqcombo", "version": "1.30.0", "sha256": "1kbx5y8cd8hvycjnqkxksr846ahfwfw31iwhbnp0hmnj88h5ckrf", "depends": ["ggplot2", "igraph", "yulab_utils"] }, "seqsetvis": { "name": "seqsetvis", "version": "1.28.0", "sha256": "1q6mq04qz7h7pfsdb9g6bpvddc0izrml4231s4g3vpynxlbjjy1i", "depends": ["GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "UpSetR", "cowplot", "data_table", "eulerr", "ggplot2", "ggplotify", "limma", "pbapply", "pbmcapply", "png", "rtracklayer", "scales"] }, "sesame": { "name": "sesame", "version": "1.26.0", "sha256": "0kc5xs0cawxvp6qfrnppkaqx8s52j04cx6cypp05gykq8pyywpyn", "depends": ["BiocFileCache", "BiocParallel", "GenomeInfoDb", "GenomicRanges", "IRanges", "MASS", "S4Vectors", "SummarizedExperiment", "dplyr", "ggplot2", "preprocessCore", "readr", "reshape2", "sesameData", "stringr", "tibble", "wheatmap"] }, "sevenC": { "name": "sevenC", "version": "1.28.0", "sha256": "1r0ibaa29dlrz0zjszq7gnbk3dkis2djmzf8vkwqqncsfp1fm0dj", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "InteractionSet", "S4Vectors", "boot", "data_table", "purrr", "readr", "rtracklayer"] }, "sevenbridges": { "name": "sevenbridges", "version": "1.38.0", "sha256": "14c93pljg97rnrrcm45qgjfgdzhic02k13qc072lrdyr33imyh9c", "depends": ["S4Vectors", "curl", "data_table", "docopt", "httr", "jsonlite", "objectProperties", "stringr", "uuid", "yaml"] }, "shiny_gosling": { "name": "shiny.gosling", "version": "1.4.0", "sha256": "1as7hrs3kfwxlr9zykdm88gv985gdnmzlrb2hn9zcgsalika53in", "depends": ["digest", "fs", "htmltools", "jsonlite", "rjson", "rlang", "shiny", "shiny_react"] }, "shinyDSP": { "name": "shinyDSP", "version": "1.0.3", "sha256": "00ha1cjk5g70szzxnani43ixgim43mrg89nf8rrqimvwsbbzndbn", "depends": ["AnnotationHub", "BiocGenerics", "ComplexHeatmap", "DT", "ExperimentHub", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "bsicons", "bslib", "circlize", "cowplot", "dplyr", "edgeR", "ggplot2", "ggpubr", "ggrepel", "htmltools", "limma", "magrittr", "pals", "readr", "scales", "scater", "shiny", "shinyWidgets", "shinycssloaders", "shinyjs", "shinyvalidate", "standR", "stringr", "tibble", "tidyr", "withr"] }, "shinyMethyl": { "name": "shinyMethyl", "version": "1.44.0", "sha256": "1z3ymzjy95qiv3cxgdvvjk98dilbpq218ffa8kdchh9synxwy9m5", "depends": ["Biobase", "BiocGenerics", "MatrixGenerics", "RColorBrewer", "htmltools", "minfi", "shiny"] }, "shinyepico": { "name": "shinyepico", "version": "1.16.0", "sha256": "1kpn4zhs0dqf7n1875cpphvhd6shdihrcay34x5a57d4xwyw76p4", "depends": ["DT", "GenomicRanges", "data_table", "doParallel", "dplyr", "foreach", "ggplot2", "gplots", "heatmaply", "limma", "minfi", "plotly", "reshape2", "rlang", "rmarkdown", "rtracklayer", "shiny", "shinyWidgets", "shinycssloaders", "shinyjs", "shinythemes", "statmod", "tidyr", "zip"] }, "sigFeature": { "name": "sigFeature", "version": "1.26.0", "sha256": "01wq4nrgzd52jclablzl4hpzd4a0vd38kyk5xafxqns856icw68v", "depends": ["BiocParallel", "Matrix", "RColorBrewer", "SparseM", "SummarizedExperiment", "biocViews", "e1071", "nlme", "openxlsx", "pheatmap"] }, "siggenes": { "name": "siggenes", "version": "1.82.0", "sha256": "1riccriz288gwyjq1gv1gw162mk2qfx0in67dia4xy9q7p4krjz9", "depends": ["Biobase", "multtest", "scrime"] }, "sights": { "name": "sights", "version": "1.34.0", "sha256": "1ipkmqx79j777frqi3l316jxbbd0a1npckwrj2x44jmhs4mzk4zj", "depends": ["MASS", "ggplot2", "lattice", "qvalue", "reshape2"] }, "signatureSearch": { "name": "signatureSearch", "version": "1.22.0", "sha256": "0w8yz6z8pl0qy1nlmaygdmcl57k5bb9hnqglnbs2pr6krkvw9qgi", "depends": ["AnnotationDbi", "BiocGenerics", "BiocParallel", "DOSE", "DelayedArray", "ExperimentHub", "GSEABase", "HDF5Array", "Matrix", "RSQLite", "Rcpp", "SummarizedExperiment", "clusterProfiler", "data_table", "dplyr", "fastmatch", "fgsea", "ggplot2", "magrittr", "org_Hs_eg_db", "qvalue", "reactome_db", "readr", "reshape2", "rhdf5", "scales", "tibble", "visNetwork"] }, "signeR": { "name": "signeR", "version": "2.10.0", "sha256": "0gp2r0r9bhm62zk5zxbwfz13dszsy2w4n24ldl8643mgjdi4fzwr", "depends": ["BSgenome", "BiocFileCache", "BiocGenerics", "Biostrings", "DT", "GenomeInfoDb", "GenomicRanges", "IRanges", "MASS", "NMF", "PMCMRplus", "RColorBrewer", "Rcpp", "RcppArmadillo", "VGAM", "VariantAnnotation", "ada", "bsplus", "class", "clue", "cowplot", "dplyr", "e1071", "future", "future_apply", "ggplot2", "ggpubr", "glmnet", "kknn", "listenv", "magrittr", "maxstat", "nloptr", "pROC", "pheatmap", "ppclust", "proxy", "pvclust", "randomForest", "readr", "reshape2", "rtracklayer", "scales", "shiny", "shinyWidgets", "shinycssloaders", "shinydashboard", "survival", "survivalAnalysis", "survminer", "tibble", "tidyr"] }, "signifinder": { "name": "signifinder", "version": "1.10.0", "sha256": "1kdlisb2ap7w1fblyqrnpmdn6q2w8vbxc2y4x80p9g75xgjsl8xa", "depends": ["AnnotationDbi", "BiocGenerics", "ComplexHeatmap", "DGEobj_utils", "GSVA", "IRanges", "RColorBrewer", "SpatialExperiment", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "consensusOV", "cowplot", "dplyr", "ensembldb", "ggplot2", "ggridges", "magrittr", "matrixStats", "maxstat", "openair", "org_Hs_eg_db", "patchwork", "scales", "survival", "survminer", "viridis"] }, "sigsquared": { "name": "sigsquared", "version": "1.40.0", "sha256": "10vmbip6g5cqplhiypzrnxq9fb5vyl18y75c955v49jvhyi29sg9", "depends": ["Biobase", "survival"] }, "simPIC": { "name": "simPIC", "version": "1.4.0", "sha256": "17chy5k314s876lpraga7981r1ny9ix30vjilnw69rxz18sdnp65", "depends": ["BiocGenerics", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "actuar", "checkmate", "fitdistrplus", "matrixStats", "rlang", "scales", "scuttle"] }, "similaRpeak": { "name": "similaRpeak", "version": "1.40.0", "sha256": "0pi5drniv1chj83vbvpm14ssn3s36z9cn2623yv9sqylycyjgl6s", "depends": ["R6"] }, "simona": { "name": "simona", "version": "1.6.0", "sha256": "0d6zyjcrszyavpms883hjh68zwyq5hr0jh3lnhcy2zzkzlz857fd", "depends": ["ComplexHeatmap", "GetoptLong", "GlobalOptions", "Polychrome", "Rcpp", "S4Vectors", "circlize", "igraph", "matrixStats", "shiny", "xml2"] }, "simpleSeg": { "name": "simpleSeg", "version": "1.10.1", "sha256": "1ygp3ij55fifbscy823fr3j0097yp2kj31zv7gb25jickl0p15fd", "depends": ["BiocParallel", "EBImage", "S4Vectors", "SummarizedExperiment", "cytomapper", "spatstat_geom", "terra"] }, "simplifyEnrichment": { "name": "simplifyEnrichment", "version": "2.2.0", "sha256": "11d3hw43g54x0hind177imgj15n1xjsjcngfa5k1nyc14fv3n2wi", "depends": ["AnnotationDbi", "ComplexHeatmap", "GO_db", "GetoptLong", "GlobalOptions", "circlize", "clue", "cluster", "colorspace", "digest", "simona", "slam", "tm"] }, "sincell": { "name": "sincell", "version": "1.40.0", "sha256": "1y3ylnnbmryxsdwlbmb3848kzjzvfhdrq7qwmcwkvj4cnffygmgc", "depends": ["MASS", "Rcpp", "Rtsne", "TSP", "cluster", "entropy", "fastICA", "fields", "ggplot2", "igraph", "proxy", "reshape2", "scatterplot3d", "statmod"] }, "singleCellTK": { "name": "singleCellTK", "version": "2.18.1", "sha256": "02b7wscz4r38rckbf3y1pjk94kkmvs3l8v1yb7ywgyk319hg6ig3", "depends": ["AnnotationHub", "Biobase", "BiocParallel", "ComplexHeatmap", "DESeq2", "DT", "DelayedArray", "DelayedMatrixStats", "DropletUtils", "ExperimentHub", "GSEABase", "GSVA", "GSVAdata", "KernSmooth", "MAST", "Matrix", "ROCR", "R_utils", "Rtsne", "S4Vectors", "Seurat", "SingleCellExperiment", "SingleR", "SoupX", "SummarizedExperiment", "TENxPBMCData", "TSCAN", "TrajectoryUtils", "VAM", "anndata", "ape", "batchelor", "celda", "celldex", "circlize", "cluster", "colorspace", "colourpicker", "cowplot", "data_table", "dplyr", "eds", "enrichR", "ensembldb", "fields", "ggplot2", "ggplotify", "ggrepel", "ggtree", "gridExtra", "igraph", "limma", "magrittr", "matrixStats", "metap", "msigdbr", "multtest", "plotly", "plyr", "reshape2", "reticulate", "rlang", "rmarkdown", "scDblFinder", "scMerge", "scRNAseq", "scater", "scds", "scran", "scuttle", "shiny", "shinyalert", "shinycssloaders", "shinyjs", "stringr", "sva", "tibble", "tidyr", "tximport", "withr", "yaml", "zellkonverter", "zinbwave"] }, "singscore": { "name": "singscore", "version": "1.28.0", "sha256": "122j7k42l5h1nvi91x7vgd8lnda7x353ygmvx3h98dxbxpacpvi4", "depends": ["Biobase", "BiocParallel", "GSEABase", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "edgeR", "ggplot2", "ggrepel", "magrittr", "matrixStats", "plotly", "plyr", "reshape", "reshape2", "tidyr"] }, "sitadela": { "name": "sitadela", "version": "1.16.0", "sha256": "0gqr0c2npz97imhw7a20lx4qp3kdlwp9r4zmb3j8g4hdzxhy57kw", "depends": ["Biobase", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RSQLite", "Rsamtools", "S4Vectors", "biomaRt", "rtracklayer", "txdbmaker"] }, "sitePath": { "name": "sitePath", "version": "1.24.0", "sha256": "18sjabmiiigwr4cz8b0hn415hcb12qgw5mgvdsay1al4djz33n2d", "depends": ["RColorBrewer", "Rcpp", "ape", "aplot", "ggplot2", "ggrepel", "ggtree", "gridExtra", "seqinr", "tidytree"] }, "sizepower": { "name": "sizepower", "version": "1.78.0", "sha256": "0g776gfipp2gd1k7ad77vznwcydly7j5a350vk59dk75c8mxc84k", "depends": [] }, "sketchR": { "name": "sketchR", "version": "1.4.0", "sha256": "0ykm74i292rdavdahhyb9gr92gc92pz8f49795klm1dfa3m50bzg", "depends": ["Biobase", "DelayedArray", "basilisk", "dplyr", "ggplot2", "reticulate", "rlang", "scales"] }, "skewr": { "name": "skewr", "version": "1.40.0", "sha256": "11mivap26raymy9xyxd5fk9abgdnfj0f91w2y8mychf63yp02fql", "depends": ["IlluminaHumanMethylation450kmanifest", "RColorBrewer", "S4Vectors", "methylumi", "minfi", "mixsmsn", "wateRmelon"] }, "slalom": { "name": "slalom", "version": "1.30.0", "sha256": "03489wmi7yh23vgrvpwj4czaxvq757lnmi3kr9cv0mcqzgw2way1", "depends": ["BH", "GSEABase", "Rcpp", "RcppArmadillo", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "rsvd"] }, "slingshot": { "name": "slingshot", "version": "2.16.0", "sha256": "17s9rmd5dsw65cl218sxz5wg1ysqbwqmvcs3vyffl48j5mmsvqgm", "depends": ["S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "TrajectoryUtils", "igraph", "matrixStats", "princurve"] }, "smartid": { "name": "smartid", "version": "1.4.0", "sha256": "02z5zh03p8kq0blfacl2a299mxq5zjqr05y1zmlc26zlvwp3kvbg", "depends": ["Matrix", "SummarizedExperiment", "dplyr", "ggplot2", "mclust", "mixtools", "sparseMatrixStats", "tidyr"] }, "smoothclust": { "name": "smoothclust", "version": "1.4.0", "sha256": "1zb780asdxzpk6s7286r43zn77k9rnxcc1m02hz67a10nc1wsbxr", "depends": ["SpatialExperiment", "SummarizedExperiment", "sparseMatrixStats", "spdep"] }, "smoppix": { "name": "smoppix", "version": "1.0.0", "sha256": "0jv3rwq73apdh2dsafca95c2kl7lnm3dnrisahmk3afa31g85cs3", "depends": ["BiocParallel", "Matrix", "Rcpp", "Rdpack", "SpatialExperiment", "SummarizedExperiment", "extraDistr", "ggplot2", "lme4", "lmerTest", "openxlsx", "scam", "spatstat_geom", "spatstat_model", "spatstat_random"] }, "snapcount": { "name": "snapcount", "version": "1.20.0", "sha256": "1r7gzwrydn7b5bh34jsfy25mgppz4vrzgj1f4xbbwl43fd0np64q", "depends": ["GenomicRanges", "IRanges", "Matrix", "R6", "SummarizedExperiment", "assertthat", "data_table", "httr", "jsonlite", "magrittr", "purrr", "rlang", "stringr"] }, "snifter": { "name": "snifter", "version": "1.18.1", "sha256": "165fs7f2lwhzvbb6i2vz5l4h7fl2gc5dvqkjbzj3prdqw3rhgmig", "depends": ["assertthat", "basilisk", "irlba", "reticulate"] }, "snm": { "name": "snm", "version": "1.56.0", "sha256": "0hhq5818aicmyiq61l33xw0a7131zl3pzyg8v643va0a6bhfci99", "depends": ["corpcor", "lme4"] }, "snpStats": { "name": "snpStats", "version": "1.58.0", "sha256": "04p7dsyd1s9nxzg0fjwvxq7r1k94ncksbn0kk7s0ja8qq6lf8zgz", "depends": ["BiocGenerics", "Matrix", "survival", "zlibbioc"] }, "soGGi": { "name": "soGGi", "version": "1.40.1", "sha256": "0qz7ilxxp8f9yi2bhp7w6nk8jrakmp8ymi0r7zqzmr2ldjp03ans", "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "SummarizedExperiment", "chipseq", "ggplot2", "preprocessCore", "reshape2", "rtracklayer"] }, "sosta": { "name": "sosta", "version": "1.0.1", "sha256": "1nassx117qqd53jnhvhj30f419l125nyr1f68d6n9zmvzmq9kqnl", "depends": ["EBImage", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "dplyr", "ggplot2", "patchwork", "rlang", "sf", "smoothr", "spatstat_explore", "spatstat_geom", "spatstat_random", "terra"] }, "spaSim": { "name": "spaSim", "version": "1.10.0", "sha256": "1i8bi2x8q9zxg9z2wrhn8k2b6ywz5bypr9f9sml1sijwz7yr9f45", "depends": ["RANN", "SpatialExperiment", "SummarizedExperiment", "dplyr", "ggplot2", "spatstat_geom", "spatstat_random"] }, "spacexr": { "name": "spacexr", "version": "1.0.0", "sha256": "1pxwinam181g1lxdygjh7rw25h902nckybvj8937fqp91l6ays9c", "depends": ["BiocFileCache", "BiocParallel", "Matrix", "SpatialExperiment", "SummarizedExperiment", "ggplot2", "httr", "memoise", "quadprog", "scatterpie"] }, "sparrow": { "name": "sparrow", "version": "1.14.0", "sha256": "0vkx1917k7k63hj67dkbhmq69f0l07b0kba4mqh5syklqmgbxv9r", "depends": ["BiocGenerics", "BiocParallel", "BiocSet", "ComplexHeatmap", "DelayedMatrixStats", "GSEABase", "Matrix", "babelgene", "checkmate", "circlize", "data_table", "edgeR", "ggplot2", "irlba", "limma", "plotly", "viridis"] }, "sparseMatrixStats": { "name": "sparseMatrixStats", "version": "1.20.0", "sha256": "1xds5h7scmas1fpanmyqk9mw1bv85hn7qfp27l577fjklyiyirvr", "depends": ["Matrix", "MatrixGenerics", "Rcpp", "matrixStats"] }, "sparsenetgls": { "name": "sparsenetgls", "version": "1.26.0", "sha256": "13xbhznpcz0danvp0xl8km23sg87arjh7rx2g56829vi0v5jlh4x", "depends": ["MASS", "Matrix", "glmnet", "huge"] }, "spatialDE": { "name": "spatialDE", "version": "1.14.1", "sha256": "1fzgb08ifsgk3r0nahsn2rgfvlkfl8f1yyzarym6kfnm0pyasci8", "depends": ["Matrix", "SpatialExperiment", "SummarizedExperiment", "basilisk", "checkmate", "ggplot2", "ggrepel", "gridExtra", "reticulate", "scales"] }, "spatialFDA": { "name": "spatialFDA", "version": "1.0.0", "sha256": "0brc5cayav544bps9970yv488dc44gh471bpng0m284zwbxnxl94", "depends": ["ExperimentHub", "SpatialExperiment", "SummarizedExperiment", "dplyr", "fda", "ggplot2", "magrittr", "patchwork", "purrr", "refund", "spatstat_explore", "spatstat_geom", "tidyr"] }, "spatialHeatmap": { "name": "spatialHeatmap", "version": "2.14.1", "sha256": "002w2srp628asbwjc5q8jn51f4czrbna8raqa0sb1w7qlhckccak", "depends": ["Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "data_table", "dplyr", "edgeR", "genefilter", "ggplot2", "ggplotify", "grImport", "gridExtra", "igraph", "reshape2", "rsvg", "shiny", "shinydashboard", "spsComps", "tibble", "xml2"] }, "spatialSimGP": { "name": "spatialSimGP", "version": "1.2.0", "sha256": "0p1svv3fc6jdlbbdwrzcv3rn48nkrj25h6swh18a1iibfhpyf91y", "depends": ["MASS", "SpatialExperiment", "SummarizedExperiment"] }, "spatzie": { "name": "spatzie", "version": "1.14.0", "sha256": "1jvz4szaqx1l7n87dd68mzpgpskxarpkg36qz0nx9x0d9xv4a9jd", "depends": ["BSgenome", "BiocGenerics", "GenomeInfoDb", "GenomicFeatures", "GenomicInteractions", "GenomicRanges", "IRanges", "MatrixGenerics", "S4Vectors", "SummarizedExperiment", "TFBSTools", "ggplot2", "matrixStats", "motifmatchr"] }, "specL": { "name": "specL", "version": "1.42.0", "sha256": "00hcfxazknvnabd70l17y7mrsiyxajd3hd193krzgdrnn2cc2ynv", "depends": ["DBI", "RSQLite", "protViz", "seqinr"] }, "speckle": { "name": "speckle", "version": "1.8.0", "sha256": "0fq2z29rfzy0g4vmqhcc7rjjhk6g9n658nz3xpdmympmc0955aai", "depends": ["Seurat", "SingleCellExperiment", "edgeR", "ggplot2", "limma"] }, "spicyR": { "name": "spicyR", "version": "1.20.2", "sha256": "0whm8kwby01rrcm2ym7z5xldkb5hid11w50z1iykbjxclv1gmzcz", "depends": ["BiocParallel", "ClassifyR", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "cli", "concaveman", "coxme", "data_table", "dplyr", "ggforce", "ggh4x", "ggnewscale", "ggplot2", "ggthemes", "lifecycle", "lmerTest", "magrittr", "pheatmap", "rlang", "scam", "simpleSeg", "spatstat_explore", "spatstat_geom", "survival", "tibble", "tidyr"] }, "spikeLI": { "name": "spikeLI", "version": "2.68.0", "sha256": "0f44i5z2383v2xi7p15f947li0b63n2dmc42n27frk1g8113arrj", "depends": [] }, "spiky": { "name": "spiky", "version": "1.14.0", "sha256": "1d2dmsfg8k59n3mdsjbic7sizhylmvphskwswk41d5wrxfpw40wj", "depends": ["BSgenome", "Biostrings", "BlandAltmanLeh", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "bamlss", "ggplot2", "scales"] }, "spillR": { "name": "spillR", "version": "1.4.0", "sha256": "038i8jiwf7xavgzh4awffi3mp8rpcgismqdgjvaqbm4a6ijw3n82", "depends": ["CATALYST", "S4Vectors", "SummarizedExperiment", "dplyr", "ggplot2", "spatstat_univar", "tibble", "tidyr", "tidyselect"] }, "spkTools": { "name": "spkTools", "version": "1.64.0", "sha256": "0zy0vlvms7g3syb3fzwhnnv4fwnm8i8z1xnnjsr5y77ck8fcm74d", "depends": ["Biobase", "RColorBrewer", "gtools"] }, "splatter": { "name": "splatter", "version": "1.32.0", "sha256": "1gdmzydahqqhb2s5n1xasqcxsg60zhsmbpy0vhflkm7n6d9cr04y", "depends": ["BiocGenerics", "BiocParallel", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "checkmate", "crayon", "edgeR", "fitdistrplus", "locfit", "matrixStats", "rlang", "scuttle", "withr"] }, "splineTimeR": { "name": "splineTimeR", "version": "1.36.0", "sha256": "1zms4dn74l6liii23w2l48kq9qwkw0hl29fm6ds8vhyq21aglq25", "depends": ["Biobase", "FIs", "GSEABase", "GeneNet", "gtools", "igraph", "limma", "longitudinal"] }, "splots": { "name": "splots", "version": "1.74.0", "sha256": "1c2gk9sj49bq4cbx820lzjv7xc5apr5b51x8b3j8rr20wlfw4sj7", "depends": ["RColorBrewer"] }, "spoon": { "name": "spoon", "version": "1.4.0", "sha256": "047vz4bzhch1gik9j295xsj5b9q89fgpz3ml6s8gykp5jy1q4pyb", "depends": ["BRISC", "BiocParallel", "Matrix", "SpatialExperiment", "SummarizedExperiment", "nnSVG", "scuttle"] }, "spqn": { "name": "spqn", "version": "1.20.0", "sha256": "1b32mxiprh66fiddxz7m3ivmv1263b4xlxvpr2435zmlh9p0hajc", "depends": ["BiocGenerics", "SummarizedExperiment", "ggplot2", "ggridges", "matrixStats"] }, "squallms": { "name": "squallms", "version": "1.2.0", "sha256": "1pxr4d9mk430f9ag34gfl8vddpl6ax44q3zxfivl3is9m4153yvb", "depends": ["MSnbase", "MsExperiment", "RaMS", "caret", "data_table", "dplyr", "ggplot2", "keys", "plotly", "shiny", "tibble", "tidyr", "xcms"] }, "srnadiff": { "name": "srnadiff", "version": "1.28.0", "sha256": "0vxxavx8iqxygr61nnvsm6ggzd41z9fcpdw0lklvl1lpa300bg10", "depends": ["BiocManager", "BiocParallel", "BiocStyle", "DESeq2", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "Rcpp", "Rsamtools", "S4Vectors", "SummarizedExperiment", "edgeR", "rtracklayer"] }, "ssPATHS": { "name": "ssPATHS", "version": "1.22.0", "sha256": "08975xg8h2npsc85pba7a83n39ckw29pssnsw63a9s7h7m799vdc", "depends": ["MESS", "ROCR", "SummarizedExperiment", "dml"] }, "sscu": { "name": "sscu", "version": "2.38.0", "sha256": "1ywynv66shgbhszl6hkz092fnjnvmz59khhv9bcgfs3m7g7n8qjr", "depends": ["BiocGenerics", "Biostrings", "seqinr"] }, "ssize": { "name": "ssize", "version": "1.82.0", "sha256": "0w3jgphxa0lqk8ak1s8ryfmkziknx8k0wi5f6y3syv6dags9xlmq", "depends": ["gdata", "xtable"] }, "ssrch": { "name": "ssrch", "version": "1.24.0", "sha256": "1q0skaym2qzkvrwrvjibkrfwwrixmdc5hcg38jfgv0mbw4k6l6jw", "depends": ["DT", "shiny"] }, "ssviz": { "name": "ssviz", "version": "1.42.0", "sha256": "1k0d908wjz7m854fhc8j2mikxzq0vrwh6m1d7gn0x8wj944lq0kf", "depends": ["Biostrings", "RColorBrewer", "Rsamtools", "ggplot2", "reshape"] }, "stJoincount": { "name": "stJoincount", "version": "1.10.0", "sha256": "1w482p12rcf982887fkz2zas8admi4jdxfblh4wyafjcklqjdz1b", "depends": ["Seurat", "SpatialExperiment", "SummarizedExperiment", "dplyr", "ggplot2", "magrittr", "pheatmap", "raster", "sp", "spdep"] }, "stageR": { "name": "stageR", "version": "1.30.1", "sha256": "0jm4390p9fqm2hgifkpbz0rmmmhfc1hzbz4wl0csb3s02kdjfpb5", "depends": ["SummarizedExperiment"] }, "standR": { "name": "standR", "version": "1.12.0", "sha256": "0k5jq5jr3yi36w32pcqh700s5i8iqnfjwn8kxp6mb0l8rnrpqrwl", "depends": ["Biobase", "BiocGenerics", "RUVSeq", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "dplyr", "edgeR", "ggalluvial", "ggplot2", "limma", "mclustcomp", "patchwork", "readr", "rlang", "ruv", "tibble", "tidyr"] }, "statTarget": { "name": "statTarget", "version": "1.38.0", "sha256": "1scs6hpz1n9w36lgpl2hzyq53iif8g5w4xyln5bxfyysgsaq9gs2", "depends": ["ROC", "impute", "pdist", "pls", "plyr", "randomForest", "rrcov"] }, "stepNorm": { "name": "stepNorm", "version": "1.80.0", "sha256": "0jymh5jpkwzlihnrmbzxv12qdi0l3lqv7hp66bviixvl8waz182v", "depends": ["MASS", "marray"] }, "strandCheckR": { "name": "strandCheckR", "version": "1.26.0", "sha256": "0iig82sx2h50gan3b3af79af8m32vfhxxr8q9c94dfmk3vyy0yck", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "TxDb_Hsapiens_UCSC_hg38_knownGene", "dplyr", "ggplot2", "gridExtra", "reshape2", "rlang", "stringr", "tidyselect"] }, "struct": { "name": "struct", "version": "1.20.2", "sha256": "0280k9mv8q46fh78yhr5hxp5xayszl0q8qn39xhndin7i50pwni3", "depends": ["S4Vectors", "SummarizedExperiment", "knitr", "ontologyIndex", "rols"] }, "structToolbox": { "name": "structToolbox", "version": "1.20.0", "sha256": "1wy0bw3a6q11w1fi4i17kswfjql9865rim1znhrmfq91vqndqldp", "depends": ["ggplot2", "ggthemes", "gridExtra", "scales", "sp", "struct"] }, "subSeq": { "name": "subSeq", "version": "1.38.0", "sha256": "1x65q9bjypsr7ph68q2wl0aqjwsh5xrjzs1c7zjpl0rxrwwm3p3r", "depends": ["Biobase", "data_table", "digest", "dplyr", "ggplot2", "magrittr", "qvalue", "tidyr"] }, "supersigs": { "name": "supersigs", "version": "1.16.0", "sha256": "0l1mqpjv3qparkpraghbxxf2gf8i5mfllsgfyaaagx6bf4v6rxw9", "depends": ["Biostrings", "SummarizedExperiment", "assertthat", "caret", "dplyr", "rlang", "rsample", "tidyr"] }, "surfaltr": { "name": "surfaltr", "version": "1.14.0", "sha256": "0lxgkzl3ygdv8s1f455fqzj77sljkqqxlp87pqan6pwcbapipl7a", "depends": ["Biostrings", "biomaRt", "dplyr", "ggplot2", "httr", "msa", "protr", "readr", "seqinr", "stringr", "testthat", "xml2"] }, "survClust": { "name": "survClust", "version": "1.2.0", "sha256": "1yf74rbqbqz8pqkm3nld9l9a7jrz0scfc6cqxs1ji55yqjyhy4vw", "depends": ["MultiAssayExperiment", "Rcpp", "pdist", "survival"] }, "survcomp": { "name": "survcomp", "version": "1.58.0", "sha256": "0ddxikvaihig2vvqcc3w223kvq7mrqmsswihr6x4rhs6f78v383h", "depends": ["KernSmooth", "SuppDists", "bootstrap", "ipred", "prodlim", "rmeta", "survival", "survivalROC"] }, "survtype": { "name": "survtype", "version": "1.24.0", "sha256": "0qwwapqq8m0rdrgknyww59hmg8qn50dlngvz4a9hasxh4rnbph08", "depends": ["SummarizedExperiment", "clustvarsel", "pheatmap", "survival", "survminer"] }, "sva": { "name": "sva", "version": "3.56.0", "sha256": "0l02ckbvvgxw266rxx7cbmsr436yr4jf43b18kbnpl666i3dlxix", "depends": ["BiocParallel", "edgeR", "genefilter", "limma", "matrixStats", "mgcv"] }, "svaNUMT": { "name": "svaNUMT", "version": "1.14.0", "sha256": "12b5yfdlxk6bnkhhp67vlq2ias1rsyzq529a19cr2piz6wn5iw2s", "depends": ["BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "S4Vectors", "StructuralVariantAnnotation", "VariantAnnotation", "assertthat", "dplyr", "pwalign", "rlang", "rtracklayer", "stringr"] }, "svaRetro": { "name": "svaRetro", "version": "1.14.0", "sha256": "0b2afyjrqwbyi2p8v07qgfimd234ycjk972y0jqnay1ryma84ql8", "depends": ["BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "S4Vectors", "StructuralVariantAnnotation", "VariantAnnotation", "assertthat", "dplyr", "rlang", "rtracklayer", "stringr"] }, "swfdr": { "name": "swfdr", "version": "1.34.0", "sha256": "12sqy09l95gidc7fcplhnacm7d0wx20yzddnphymxd0mh188qnmv", "depends": [] }, "switchBox": { "name": "switchBox", "version": "1.44.0", "sha256": "1w9nzcwrdxs042yyf1ic12crb5w8ylyyn35nd5xiicszyih9vwgg", "depends": ["gplots", "pROC"] }, "switchde": { "name": "switchde", "version": "1.34.0", "sha256": "0a97mlyhxnmv4ahnk2wbjngjy80c02yq2ch001j1vfpvp3jrk3y1", "depends": ["SingleCellExperiment", "SummarizedExperiment", "dplyr", "ggplot2"] }, "synapsis": { "name": "synapsis", "version": "1.14.0", "sha256": "1253f4k4zw0cwcgkw492mf45m63pak6z40k1w6p5yaszn4nggib7", "depends": ["EBImage"] }, "synapter": { "name": "synapter", "version": "2.31.0", "sha256": "09jcnaw6mhcwk1mzysk3ryy6j11dasj3dkz7gajlgm855wcznkmp", "depends": ["Biobase", "Biostrings", "MSnbase", "RColorBrewer", "cleaver", "lattice", "multtest", "qvalue", "readr", "rmarkdown"] }, "synergyfinder": { "name": "synergyfinder", "version": "3.16.0", "sha256": "0023giyw9jms8h6wx8fs1lkzq16q6i7x9kh222qxjrn7d75ccp5h", "depends": ["SpatialExtremes", "dplyr", "drc", "furrr", "future", "ggforce", "ggplot2", "ggrepel", "gstat", "kriging", "lattice", "magrittr", "metR", "mice", "nleqslv", "pbapply", "plotly", "purrr", "reshape2", "sp", "stringr", "tidyr", "tidyverse", "vegan"] }, "synlet": { "name": "synlet", "version": "2.8.0", "sha256": "0zfwzblj1ch5ijc72ckslhhwiing005hzmkv0q0zd81rpyadpw5z", "depends": ["RColorBrewer", "RankProd", "data_table", "ggplot2", "magrittr", "patchwork"] }, "syntenet": { "name": "syntenet", "version": "1.10.2", "sha256": "0lxjxcx08n30s72n7sdpzssb1faxsclvd4rmd0gqfvh331y3j70q", "depends": ["BiocParallel", "Biostrings", "GenomicRanges", "RColorBrewer", "Rcpp", "ggnetwork", "ggplot2", "igraph", "intergraph", "pheatmap", "rlang", "testthat"] }, "systemPipeR": { "name": "systemPipeR", "version": "2.14.2", "sha256": "0l3h2n1705y33n1l9cgxbf9dlx6aksk7r9h55jdb6jbz3wcwqlzq", "depends": ["BiocGenerics", "Biostrings", "GenomicRanges", "Rsamtools", "S4Vectors", "ShortRead", "SummarizedExperiment", "crayon", "ggplot2", "htmlwidgets", "magrittr", "stringr", "yaml"] }, "systemPipeShiny": { "name": "systemPipeShiny", "version": "1.18.0", "sha256": "0z459cr5jcnrirdjf8n4bzv1ai053vg1bq1vcn2v6ykavpghrk84", "depends": ["DT", "R6", "RSQLite", "assertthat", "bsplus", "crayon", "dplyr", "drawer", "ggplot2", "glue", "htmltools", "magrittr", "openssl", "plotly", "rlang", "rstudioapi", "shiny", "shinyAce", "shinyFiles", "shinyWidgets", "shinydashboard", "shinydashboardPlus", "shinyjqui", "shinyjs", "shinytoastr", "spsComps", "spsUtil", "stringr", "styler", "tibble", "vroom", "yaml"] }, "systemPipeTools": { "name": "systemPipeTools", "version": "1.16.0", "sha256": "0kmi6rj0cqdhpc673ai0knwzyvy7mvizjw33aw6hlnd2ry35iclj", "depends": ["DESeq2", "DT", "GGally", "Rtsne", "SummarizedExperiment", "ape", "dplyr", "ggplot2", "ggrepel", "ggtree", "glmpca", "magrittr", "pheatmap", "plotly", "tibble"] }, "tLOH": { "name": "tLOH", "version": "1.16.0", "sha256": "11yn96yb3i4kwqp41qdcgwj771xzdvrgwycdsxm83zycc38lqsdh", "depends": ["GenomicRanges", "MatrixGenerics", "VariantAnnotation", "bestNormalize", "data_table", "depmixS4", "dplyr", "ggplot2", "naniar", "purrr", "scales", "stringr"] }, "tRNA": { "name": "tRNA", "version": "1.26.0", "sha256": "1b39fyfg3kn0dadq1apq25rqmszf4mb58kz9jiq3fdss3sxl316j", "depends": ["BiocGenerics", "Biostrings", "GenomicRanges", "IRanges", "Modstrings", "S4Vectors", "Structstrings", "XVector", "ggplot2", "scales", "stringr"] }, "tRNAdbImport": { "name": "tRNAdbImport", "version": "1.26.0", "sha256": "0ldrn67kjzjzndjyx3zx3a0s1dglkz2g57yrm5f9wg9gjdgqy44n", "depends": ["Biostrings", "GenomicRanges", "IRanges", "Modstrings", "S4Vectors", "Structstrings", "httr2", "stringr", "tRNA", "xml2"] }, "tRNAscanImport": { "name": "tRNAscanImport", "version": "1.28.0", "sha256": "0zzkk6p7jw1z06faj55h8qqh0n8xm2x5i062f55b6nggfk5kam26", "depends": ["BSgenome", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Structstrings", "XVector", "rtracklayer", "stringr", "tRNA"] }, "tRanslatome": { "name": "tRanslatome", "version": "1.46.0", "sha256": "041f3p900nxgdgj3dlas7wjlr6ix5qck01ccmq15cm4bspb3fw0g", "depends": ["Biobase", "DESeq2", "GOSemSim", "Heatplus", "RankProd", "anota", "edgeR", "gplots", "limma", "org_Hs_eg_db", "plotrix", "topGO"] }, "tadar": { "name": "tadar", "version": "1.6.0", "sha256": "0rnmsnd0k6psh69d11bcz2khx0ppqd92fn9lgnsayvx2kayayj50", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "Gviz", "IRanges", "MatrixGenerics", "Rsamtools", "S4Vectors", "VariantAnnotation", "ggplot2", "lifecycle", "rlang"] }, "tanggle": { "name": "tanggle", "version": "1.14.0", "sha256": "0v461653bm3sik6d1sy8ad87vkyl94yk60n3civ696j15mnk0rlx", "depends": ["ape", "ggplot2", "ggtree", "phangorn"] }, "target": { "name": "target", "version": "1.22.0", "sha256": "00338jl5yw4g2g8kbkwaln7gxyvg21f4x61ng861ln3g4sad4c5v", "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "matrixStats", "shiny"] }, "tenXplore": { "name": "tenXplore", "version": "1.30.0", "sha256": "0svqk2hcp3dkqa0r94yll17lzjxwnld5ci04k5fmjm28234770f0", "depends": ["AnnotationDbi", "BiocFileCache", "SummarizedExperiment", "matrixStats", "ontoProc", "org_Mm_eg_db", "shiny"] }, "terapadog": { "name": "terapadog", "version": "1.0.0", "sha256": "0kbbcylr8f99gp2877lcjk786zasvjbjgzgyyrd0zg26r7c4jwzh", "depends": ["DESeq2", "KEGGREST", "biomaRt", "dplyr", "htmlwidgets", "plotly"] }, "ternarynet": { "name": "ternarynet", "version": "1.52.0", "sha256": "0a33srg37npd4x8y80s397ca49vfaslmi0mkldabr5kfyp4gpgib", "depends": ["BiocParallel", "igraph"] }, "terraTCGAdata": { "name": "terraTCGAdata", "version": "1.12.0", "sha256": "0cf0ai3bdpz0xn2fk37lc1iyq3b2yk5k3f63hhhwya0k551liwll", "depends": ["AnVIL", "AnVILGCP", "BiocFileCache", "GenomicRanges", "MultiAssayExperiment", "RaggedExperiment", "S4Vectors", "TCGAutils", "dplyr", "readr", "tidyr"] }, "tidyCoverage": { "name": "tidyCoverage", "version": "1.4.1", "sha256": "1gjk7qb6ckg64nfscx0cjhz14ivrxzg5rcjwv6nzyv4kc049w38n", "depends": ["BiocIO", "BiocParallel", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "cli", "dplyr", "fansi", "ggplot2", "pillar", "purrr", "rlang", "rtracklayer", "scales", "tidyr", "vctrs"] }, "tidyFlowCore": { "name": "tidyFlowCore", "version": "1.2.0", "sha256": "18nfv2i0kwv12mam2cja8pfja8amgj9ap5lpvp42zqhvjskgms4c", "depends": ["Biobase", "dplyr", "flowCore", "ggplot2", "purrr", "rlang", "stringr", "tibble", "tidyr"] }, "tidySingleCellExperiment": { "name": "tidySingleCellExperiment", "version": "1.18.1", "sha256": "12fbw9l2c8jjchicba17qbjbrgz1l0mw4idvfpfrldh4gp4yprnm", "depends": ["Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "cli", "dplyr", "ellipsis", "fansi", "ggplot2", "lifecycle", "magrittr", "pillar", "pkgconfig", "purrr", "rlang", "stringr", "tibble", "tidyr", "tidyselect", "ttservice", "vctrs"] }, "tidySpatialExperiment": { "name": "tidySpatialExperiment", "version": "1.4.1", "sha256": "1cb0g0v6141c1kkq4w7qgihm5d145bxfnwg7zwaql19zw9zvizlm", "depends": ["BiocGenerics", "Matrix", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "cli", "dplyr", "fansi", "ggplot2", "lifecycle", "magick", "pillar", "pkgconfig", "plotly", "purrr", "rlang", "shiny", "stringr", "tibble", "tidySingleCellExperiment", "tidygate", "tidyr", "tidyselect", "ttservice", "vctrs"] }, "tidySummarizedExperiment": { "name": "tidySummarizedExperiment", "version": "1.18.1", "sha256": "1x0hznrycafn6n3mn4sr15974pvy7xzdhk3njv7qrrwvv6wqyyfq", "depends": ["S4Vectors", "SummarizedExperiment", "cli", "dplyr", "ellipsis", "fansi", "ggplot2", "lifecycle", "magrittr", "pillar", "pkgconfig", "purrr", "rlang", "stringr", "tibble", "tidyr", "tidyselect", "ttservice", "vctrs"] }, "tidybulk": { "name": "tidybulk", "version": "1.20.0", "sha256": "0mpinpa29f1rzcch9vwjfhifsmzf8if0dg2ahqzpri074ih29abz", "depends": ["GenomicRanges", "Matrix", "S4Vectors", "SummarizedExperiment", "crayon", "dplyr", "lifecycle", "magrittr", "preprocessCore", "purrr", "readr", "rlang", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "ttservice"] }, "tidyomics": { "name": "tidyomics", "version": "1.4.0", "sha256": "18imvbc8dcqn5iykp1gd73ndw39jyf8lymcafhlpswww9ibw2cb5", "depends": ["cli", "nullranges", "plyranges", "purrr", "rlang", "stringr", "tidySingleCellExperiment", "tidySummarizedExperiment", "tidybulk", "tidyseurat"] }, "tidysbml": { "name": "tidysbml", "version": "1.2.0", "sha256": "0yp08108r1njxg4dfvn7g9ccqxq0by2alxqdmy29j55ky482inz5", "depends": ["xml2"] }, "tidytof": { "name": "tidytof", "version": "1.2.0", "sha256": "13m028bm21j7404ncvpg7l7qvfkbvcnbrf4rp3xilyl5m6cyvidy", "depends": ["Rcpp", "RcppHNSW", "doParallel", "dplyr", "flowCore", "foreach", "ggplot2", "ggraph", "glmnet", "purrr", "readr", "recipes", "rlang", "stringr", "survival", "tibble", "tidygraph", "tidyr", "tidyselect", "yardstick"] }, "tigre": { "name": "tigre", "version": "1.62.0", "sha256": "1mhlw8swf79rymbi6343bxls33czcnv97n59inv46vj5cmax5l2m", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "DBI", "RSQLite", "annotate", "gplots"] }, "tilingArray": { "name": "tilingArray", "version": "1.86.0", "sha256": "1j5b3400xfhzdffxrq08qk1sigr17r79v27f2iwpawn395vql9a2", "depends": ["Biobase", "RColorBrewer", "affy", "genefilter", "pixmap", "strucchange", "vsn"] }, "timeOmics": { "name": "timeOmics", "version": "1.20.0", "sha256": "00nrah03r01j1n26h2gfim0cwwpajv0k54pmf0dhgmxjy7dbsdqa", "depends": ["checkmate", "dplyr", "ggplot2", "ggrepel", "lmtest", "magrittr", "mixOmics", "plyr", "purrr", "stringr", "tibble", "tidyr"] }, "timecourse": { "name": "timecourse", "version": "1.80.0", "sha256": "16w5h3mwzw9kbg4wiw2g9k2n5znx2lkrfd2scj9vp55v6px04kn3", "depends": ["Biobase", "MASS", "limma", "marray"] }, "timescape": { "name": "timescape", "version": "1.32.0", "sha256": "11wm1ad2qfkiq78z3llk9i5114i10j3mg68r0wa34s90xx765s0k", "depends": ["dplyr", "gtools", "htmlwidgets", "jsonlite", "stringr"] }, "tkWidgets": { "name": "tkWidgets", "version": "1.86.0", "sha256": "0ssq1qzlw7bbk3rxbyjbwa0y03bmpbfqgih7bl3p1b5jnr3zv9z5", "depends": ["DynDoc", "widgetTools"] }, "tomoda": { "name": "tomoda", "version": "1.18.0", "sha256": "01d8xrb35zaf0l4x8c28i1jy9yfwr5s9ngl4fxn67m2ncbg9wfpi", "depends": ["RColorBrewer", "Rtsne", "SummarizedExperiment", "ggplot2", "ggrepel", "reshape2", "umap"] }, "tomoseqr": { "name": "tomoseqr", "version": "1.12.0", "sha256": "0w8wajmxy8gk3kviqq65n1v7rnrih4c5c4ppb79hlab698i2nn9c", "depends": ["BiocFileCache", "animation", "dplyr", "ggplot2", "plotly", "purrr", "readr", "shiny", "stringr", "tibble"] }, "topGO": { "name": "topGO", "version": "2.60.1", "sha256": "059fh7z47f8pvfqaxgq5pzp3a39rvg14xw2pk0fgj8d38706l18f", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "DBI", "GO_db", "SparseM", "graph", "lattice", "matrixStats"] }, "topconfects": { "name": "topconfects", "version": "1.24.0", "sha256": "1dn4b85jbgd9jbphaxq8ziabf7r02pfv6j42nvqhfnwwxcdfxi0w", "depends": ["assertthat", "ggplot2", "scales"] }, "topdownr": { "name": "topdownr", "version": "1.30.0", "sha256": "1h6q9lqlk1h4bqww7hbhjgai3rwnhcnq946dad1xlhwdsw9yb22y", "depends": ["Biobase", "BiocGenerics", "Biostrings", "MSnbase", "Matrix", "PSMatch", "ProtGenerics", "S4Vectors", "ggplot2", "mzR"] }, "tpSVG": { "name": "tpSVG", "version": "1.4.0", "sha256": "0cxd5q1jk5whkcg486gqq90rp203j6ng3ahzvrk8aw1wg4fjzz8z", "depends": ["BiocParallel", "MatrixGenerics", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "mgcv"] }, "trackViewer": { "name": "trackViewer", "version": "1.44.0", "sha256": "0x7048mf4i55sf6wr2b1ibpiw2jpw7bdd3w6n9m0dwirg0w487qf", "depends": ["AnnotationDbi", "BiocGenerics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "InteractionSet", "Rsamtools", "S4Vectors", "grImport", "htmlwidgets", "rhdf5", "rtracklayer", "scales", "strawr", "txdbmaker"] }, "tracktables": { "name": "tracktables", "version": "1.42.0", "sha256": "10s4j4p6znqjd8bgkfis1mn75801gj2wh4zvj26r60h49dq52q6a", "depends": ["GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "XML", "XVector", "stringr", "tractor_base"] }, "tradeSeq": { "name": "tradeSeq", "version": "1.22.0", "sha256": "1vfz17rl3x777ssp0dlxxg4wb94703n31ibvxg56xbn1qvb8n0s1", "depends": ["Biobase", "BiocParallel", "MASS", "Matrix", "RColorBrewer", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "TrajectoryUtils", "edgeR", "ggplot2", "igraph", "magrittr", "matrixStats", "mgcv", "pbapply", "princurve", "slingshot", "tibble", "viridis"] }, "transcriptR": { "name": "transcriptR", "version": "1.36.0", "sha256": "182wynhpzh0ri8hxxbia4lnsr416z9j02cy4wcmw6s6wwxi6rw10", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "caret", "chipseq", "e1071", "ggplot2", "pROC", "reshape2", "rtracklayer"] }, "transcriptogramer": { "name": "transcriptogramer", "version": "1.30.0", "sha256": "00vg9f563jv0wdhyiyw1nfx1v434hhbb6g2bl6r4hvpccfjz2f3s", "depends": ["RedeR", "biomaRt", "data_table", "doSNOW", "foreach", "ggplot2", "igraph", "limma", "progress", "snow", "tidyr", "topGO"] }, "transformGamPoi": { "name": "transformGamPoi", "version": "1.14.0", "sha256": "0v6k2rppy64n80c5fpk9d1hvjsqklrzmyp5pq3qr6pxcsgg6d63d", "depends": ["DelayedArray", "HDF5Array", "Matrix", "MatrixGenerics", "Rcpp", "SummarizedExperiment", "glmGamPoi"] }, "transite": { "name": "transite", "version": "1.26.0", "sha256": "0gy1vvvfhyfxjp1pjzbrkv1hk7skbps677128dk73vw615fiv73s", "depends": ["BiocGenerics", "Biostrings", "GenomicRanges", "Rcpp", "TFMPvalue", "dplyr", "ggplot2", "gridExtra", "scales"] }, "transmogR": { "name": "transmogR", "version": "1.4.1", "sha256": "1wxr87svf3q7sdyjb4p5pink9kpcypbbchp9s5kyi3k1yg70gkj4", "depends": ["BSgenome", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "data_table", "ggplot2", "jsonlite", "matrixStats", "rlang", "scales"] }, "transomics2cytoscape": { "name": "transomics2cytoscape", "version": "1.18.0", "sha256": "0a3bnhknmj3kvkca2gssx7hv1ahiqzwdh9p8c0ijdi7ripqsv0cv", "depends": ["KEGGREST", "RCy3", "dplyr", "pbapply", "purrr", "tibble"] }, "traseR": { "name": "traseR", "version": "1.38.0", "sha256": "15xl952af9gskph0jxcj625z5g14m4r38l56gynjhsjmj9hcnfrm", "depends": ["BSgenome_Hsapiens_UCSC_hg19", "GenomicRanges", "IRanges"] }, "treeclimbR": { "name": "treeclimbR", "version": "1.4.0", "sha256": "1v7k9lzlymsc5gxchz68abx8g35l5h012cp7z640zdgz30r49v83", "depends": ["S4Vectors", "SummarizedExperiment", "TreeSummarizedExperiment", "ape", "diffcyt", "dirmult", "dplyr", "edgeR", "ggnewscale", "ggplot2", "ggtree", "rlang", "tibble", "tidyr", "viridis"] }, "treeio": { "name": "treeio", "version": "1.32.0", "sha256": "1fcr47cj4xqdscc6riyffw5a60iz5hrz87v0ajpi3nmbiab2xjpg", "depends": ["ape", "dplyr", "jsonlite", "magrittr", "rlang", "tibble", "tidytree", "yulab_utils"] }, "treekoR": { "name": "treekoR", "version": "1.16.0", "sha256": "100wzgh7bfq03k96k6k0m4xbxaas8fr04q18p5ppqrq4ywb9d0i8", "depends": ["SingleCellExperiment", "ape", "data_table", "diffcyt", "dplyr", "edgeR", "ggiraph", "ggplot2", "ggtree", "hopach", "lme4", "multcomp", "patchwork", "tidyr"] }, "tricycle": { "name": "tricycle", "version": "1.16.0", "sha256": "0s8ywy4rs9bpn3dm4mr4ml1i5c61121xzmq3n177bwsz83clkp3q", "depends": ["AnnotationDbi", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "circular", "dplyr", "ggnewscale", "ggplot2", "scater", "scattermore"] }, "trigger": { "name": "trigger", "version": "1.53.0", "sha256": "1m1gwqjz8b72csygl0yp2jz3i9pv8yxgb3gk5s53bbh27wfh9hk8", "depends": ["corpcor", "qtl", "qvalue", "sva"] }, "trio": { "name": "trio", "version": "3.46.0", "sha256": "05l4k349d7nwdbx7g89vl93sn6zqh66rxhjbaas3ffly611fycbd", "depends": ["LogicReg", "data_table", "siggenes", "survival"] }, "triplex": { "name": "triplex", "version": "1.48.0", "sha256": "1iycda6qrhiqlq1zpih6mr4ch4cl1npjwxc9dz9j2n6043afz3sv", "depends": ["Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "XVector"] }, "tripr": { "name": "tripr", "version": "1.14.0", "sha256": "0isw18lfs9dz0i5qrkdsw3vprfrd7zcqvr5726hv24pwn2irf3yk", "depends": ["DT", "RColorBrewer", "config", "data_table", "dplyr", "golem", "gridExtra", "plot3D", "plotly", "plyr", "shiny", "shinyBS", "shinyFiles", "shinyjs", "stringdist", "stringr", "vegan"] }, "ttgsea": { "name": "ttgsea", "version": "1.16.0", "sha256": "16b46a59r3rihx9w83pwqpicphk70dszri45jj0xrk4fx5kzqgzr", "depends": ["DiagrammeR", "data_table", "keras", "purrr", "stopwords", "text2vec", "textstem", "tm", "tokenizers"] }, "tweeDEseq": { "name": "tweeDEseq", "version": "1.54.0", "sha256": "1xna9h9n7q8ay4a6xbbd293qhfq5vf59vls9vb21jb0zlwig2ikl", "depends": ["MASS", "Rcpp", "cqn", "edgeR", "limma"] }, "twilight": { "name": "twilight", "version": "1.84.0", "sha256": "0kamrxihicjy1n7kwyv8zfclprxysxcj9q04wpk8cwcr1yy34vqx", "depends": ["Biobase"] }, "twoddpcr": { "name": "twoddpcr", "version": "1.32.0", "sha256": "0f8xakjz0177d2ckzrsy0kbwa9f40rlwkf8492w0x3wz9z8f71pf", "depends": ["RColorBrewer", "S4Vectors", "class", "ggplot2", "hexbin", "scales", "shiny"] }, "txcutr": { "name": "txcutr", "version": "1.14.0", "sha256": "0p8wxnpbcvrbbmkx2fnsps8sv8f77a6zk1wv8d9lcsb5fxfd2s3m", "depends": ["AnnotationDbi", "BiocGenerics", "BiocParallel", "Biostrings", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "rtracklayer", "txdbmaker"] }, "txdbmaker": { "name": "txdbmaker", "version": "1.4.2", "sha256": "1ldc53w03gzig68c3mihywdpa83li1yxkxjwb16nlf9sc283spcx", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocIO", "DBI", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RSQLite", "S4Vectors", "UCSC_utils", "biomaRt", "httr", "rjson", "rtracklayer"] }, "tximeta": { "name": "tximeta", "version": "1.26.1", "sha256": "0za6x4il9qqyrb0rf57vb2qahqdra9snfql6canmpw2ixwhhgq6n", "depends": ["AnnotationDbi", "AnnotationHub", "BiocFileCache", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "S4Vectors", "SummarizedExperiment", "ensembldb", "jsonlite", "tibble", "txdbmaker", "tximport"] }, "tximport": { "name": "tximport", "version": "1.36.1", "sha256": "1wmapwbrx43q69dv0vgajzha2hq95xb6k3bx2vxpf29d771fsv46", "depends": [] }, "uSORT": { "name": "uSORT", "version": "1.34.0", "sha256": "15hvv9vj9h2jsics6b4asbmjcm54jgqc3mgsgmgia4njr811a8vi", "depends": ["Biobase", "BiocGenerics", "Matrix", "RANN", "RSpectra", "VGAM", "cluster", "fpc", "gplots", "igraph", "monocle", "plyr"] }, "uncoverappLib": { "name": "uncoverappLib", "version": "1.18.0", "sha256": "1s4arjnwf4dq939a0k56al1lb7l02j20db58qsgys5jlmc79b5gq", "depends": ["BiocFileCache", "DT", "EnsDb_Hsapiens_v75", "EnsDb_Hsapiens_v86", "GenomicRanges", "Gviz", "Homo_sapiens", "OrganismDbi", "Rsamtools", "S4Vectors", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "condformat", "markdown", "openxlsx", "org_Hs_eg_db", "processx", "rappdirs", "rlist", "shiny", "shinyBS", "shinyWidgets", "shinycssloaders", "shinyjs", "stringr"] }, "unifiedWMWqPCR": { "name": "unifiedWMWqPCR", "version": "1.44.0", "sha256": "0dsk0nwlv2g717124rlw80w2ggmkp09mhsn1bwlz8v2yn52qzaj3", "depends": ["BiocGenerics", "limma"] }, "universalmotif": { "name": "universalmotif", "version": "1.26.2", "sha256": "14jsb54hjmbmmckbyvrv5cxdmchddfn4imq5whynbq6js18px99m", "depends": ["BiocGenerics", "Biostrings", "IRanges", "MASS", "MatrixGenerics", "Rcpp", "RcppThread", "S4Vectors", "ggplot2", "rlang", "yaml"] }, "updateObject": { "name": "updateObject", "version": "1.12.0", "sha256": "1pwfm6zibi4bcjhqrgb9yz1ixw1kmd1lmgvcv8r1iwc0wvcrvk46", "depends": ["BiocGenerics", "S4Vectors", "digest"] }, "variancePartition": { "name": "variancePartition", "version": "1.38.0", "sha256": "1kwlias43ga649xxm7mlb85s8br6d9sy2ihc31fmi4sx86c912yz", "depends": ["Biobase", "BiocParallel", "MASS", "Matrix", "Rdpack", "RhpcBLASctl", "aod", "corpcor", "fANCOVA", "ggplot2", "gplots", "iterators", "limma", "lme4", "lmerTest", "matrixStats", "pbkrtest", "remaCor", "reshape2", "rlang", "scales"] }, "vbmp": { "name": "vbmp", "version": "1.76.0", "sha256": "107fdsascnkf2sddqg6n3ncc4b2qiknhx9s74lg05lbzr2p1i12q", "depends": [] }, "velociraptor": { "name": "velociraptor", "version": "1.18.0", "sha256": "0j9gi0p2jgqhzbyfdykwdsphyjg74phdz6fw1r92qz94fs2hpis3", "depends": ["BiocGenerics", "BiocParallel", "BiocSingular", "DelayedArray", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "basilisk", "reticulate", "scuttle", "zellkonverter"] }, "veloviz": { "name": "veloviz", "version": "1.14.0", "sha256": "1n5xm73iygs8r3r75sibxinm32jh8609dy0ckghfzb0v4kliczcf", "depends": ["Matrix", "RSpectra", "Rcpp", "igraph", "mgcv"] }, "vidger": { "name": "vidger", "version": "1.28.0", "sha256": "048sdliqp19726crn1jq0cw67wm237wmcc9sn8qchii4d0fijc4z", "depends": ["Biobase", "DESeq2", "GGally", "RColorBrewer", "SummarizedExperiment", "edgeR", "ggplot2", "ggrepel", "knitr", "rmarkdown", "scales", "tidyr"] }, "viper": { "name": "viper", "version": "1.42.0", "sha256": "090j9vvsi7876hhl15bkfasbicc2rndil6ji6v66b8vk86gdclaz", "depends": ["Biobase", "KernSmooth", "e1071", "mixtools"] }, "visiumStitched": { "name": "visiumStitched", "version": "1.0.0", "sha256": "1rg0bybpbzvxz4wbq0m9fgpbvcz99gdc3dg0rg3sm1shxx1s54xf", "depends": ["BiocBaseUtils", "BiocGenerics", "DropletUtils", "Matrix", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "dplyr", "imager", "pkgcond", "readr", "rjson", "spatialLIBD", "stringr", "tibble", "tidyr", "xml2"] }, "vissE": { "name": "vissE", "version": "1.16.0", "sha256": "0a1z4zjw740p6skm0pxvb7b7x5asdjk5dg2wa12nfc7im0a6nf41", "depends": ["GSEABase", "RColorBrewer", "ggforce", "ggplot2", "ggraph", "ggrepel", "ggwordcloud", "igraph", "msigdb", "plyr", "reshape2", "scales", "scico", "textstem", "tidygraph", "tm"] }, "vmrseq": { "name": "vmrseq", "version": "1.0.1", "sha256": "1z3l0nnh8q98rj6f2ihr9jknwy4jhjbhxg9q12sf5cz32qxx554a", "depends": ["BiocParallel", "DelayedArray", "GenomicRanges", "HDF5Array", "IRanges", "S4Vectors", "SummarizedExperiment", "bumphunter", "data_table", "dplyr", "gamlss_dist", "ggplot2", "locfit", "recommenderlab", "tidyr"] }, "vsclust": { "name": "vsclust", "version": "1.10.0", "sha256": "1kackwsy9fp5dk69s89kwdspngz6ak3blffkqx2aj1yj5sbqn6c4", "depends": ["MultiAssayExperiment", "Rcpp", "limma", "matrixStats", "qvalue", "shiny"] }, "vsn": { "name": "vsn", "version": "3.76.0", "sha256": "0nv4v8j0bc7mnmd4y344rsry4wmg6rynlaablka8hb7njnq6gkh6", "depends": ["Biobase", "affy", "ggplot2", "lattice", "limma"] }, "vtpnet": { "name": "vtpnet", "version": "0.48.0", "sha256": "07fc511w8jk38blp4d81km8s71ffnshy6x8jjbfnx1vhfq4rjakj", "depends": ["GenomicRanges", "doParallel", "foreach", "graph", "gwascat"] }, "vulcan": { "name": "vulcan", "version": "1.30.0", "sha256": "0pm8kflmm26yvzxb1npas98xpc0d04inzdaf9zgxj3283mdg0ymx", "depends": ["Biobase", "ChIPpeakAnno", "DESeq2", "DiffBind", "GenomicRanges", "S4Vectors", "TxDb_Hsapiens_UCSC_hg19_knownGene", "caTools", "csaw", "gplots", "locfit", "viper", "wordcloud", "zoo"] }, "waddR": { "name": "waddR", "version": "1.22.0", "sha256": "0vc1ryyn6pvgjgay57pa8sq9q4jmc6nld4v5pn1ix0jpjmysj0mv", "depends": ["BiocFileCache", "BiocParallel", "Rcpp", "RcppArmadillo", "SingleCellExperiment", "arm", "eva"] }, "wateRmelon": { "name": "wateRmelon", "version": "2.14.0", "sha256": "0qgya8cva2942mxvwcb53rrs2s8mivg6x4m537l5hk4zvlvz20ym", "depends": ["Biobase", "IlluminaHumanMethylation450kanno_ilmn12_hg19", "ROC", "illuminaio", "limma", "lumi", "matrixStats", "methylumi"] }, "wavClusteR": { "name": "wavClusteR", "version": "2.42.0", "sha256": "1y254sq86vwcs7nz6c9p16nbrpmnshsm1k2dqfgpw7y277fkd8a9", "depends": ["BiocGenerics", "Biostrings", "GenomicFeatures", "GenomicRanges", "Hmisc", "IRanges", "Rsamtools", "S4Vectors", "foreach", "ggplot2", "mclust", "rtracklayer", "seqinr", "stringr"] }, "weaver": { "name": "weaver", "version": "1.74.0", "sha256": "1fb15gnl6kkkv2q7abx9k15jyqagqpp36gy1zvkrv7cljl3735x5", "depends": ["codetools", "digest"] }, "webbioc": { "name": "webbioc", "version": "1.80.0", "sha256": "0w3gzkhxd928k563pfy45fkgrhrgmh0prvnq6128b0vs250s3qpy", "depends": ["Biobase", "BiocManager", "affy", "annaffy", "gcrma", "multtest", "qvalue", "vsn"] }, "weitrix": { "name": "weitrix", "version": "1.20.0", "sha256": "1v11s901cnq2pj582a4j220g3z5l8b4qlxv0xhxzkah03b4vq6j4", "depends": ["BiocGenerics", "BiocParallel", "Ckmeans_1d_dp", "DelayedArray", "DelayedMatrixStats", "RhpcBLASctl", "S4Vectors", "SummarizedExperiment", "assertthat", "dplyr", "ggplot2", "glm2", "limma", "purrr", "reshape2", "rlang", "scales", "topconfects"] }, "widgetTools": { "name": "widgetTools", "version": "1.86.0", "sha256": "1b7j4fh4cnvw31fkyyfz3k8vm1y2xdsdphcqwhgx74jd6z04pvrs", "depends": [] }, "wiggleplotr": { "name": "wiggleplotr", "version": "1.32.0", "sha256": "0ncldwkyy0pd97bgv9zps9xh4b2a6apzvy9jhm5n6wgrr0i01zq2", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "assertthat", "cowplot", "dplyr", "ggplot2", "purrr", "rtracklayer"] }, "wpm": { "name": "wpm", "version": "1.18.0", "sha256": "1snwgkqi2pdwajx7maz14vipjgilxnslc59qgxaxjhfpr630i8yy", "depends": ["Biobase", "DT", "RColorBrewer", "SummarizedExperiment", "cli", "config", "dplyr", "ggplot2", "golem", "logging", "rlang", "shiny", "shinyWidgets", "shinycustomloader", "shinydashboard", "stringr"] }, "wppi": { "name": "wppi", "version": "1.16.0", "sha256": "17rkfbhy0r22ayca4c7n8gr2kjgbj3r4gk1rh423cp566x0n7pcp", "depends": ["Matrix", "OmnipathR", "RCurl", "dplyr", "igraph", "logger", "magrittr", "progress", "purrr", "rlang", "tibble", "tidyr"] }, "xCell2": { "name": "xCell2", "version": "1.0.9", "sha256": "1k1ab1rsiwzfagf0hd718mrxk5qwc47qjvf2qq3wqvv5fbpq0iqv", "depends": ["AnnotationHub", "BiocParallel", "Matrix", "Rfast", "SingleCellExperiment", "SummarizedExperiment", "dplyr", "magrittr", "minpack_lm", "ontologyIndex", "pracma", "progress", "quadprog", "readr", "singscore", "tibble", "tidyselect"] }, "xcms": { "name": "xcms", "version": "4.6.3", "sha256": "12cylv5gfbxjf6y64hrl76h55j30xc1fc7qvsv5vj0xynxa92lyy", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "IRanges", "MSnbase", "MassSpecWavelet", "MetaboCoreUtils", "MsCoreUtils", "MsExperiment", "MsFeatures", "ProtGenerics", "RColorBrewer", "S4Vectors", "Spectra", "SummarizedExperiment", "lattice", "mzR", "progress"] }, "xcore": { "name": "xcore", "version": "1.12.0", "sha256": "1i17xqa5gyhhwa98dcfbc5nihwrql4ndpp7prcxvzwiahcgghxay", "depends": ["DelayedArray", "GenomicRanges", "IRanges", "Matrix", "MultiAssayExperiment", "S4Vectors", "edgeR", "foreach", "glmnet", "iterators", "magrittr"] }, "xenLite": { "name": "xenLite", "version": "1.2.1", "sha256": "1ymbcb2w5997qhai5jpavqb1dk73bhg3c1m3bxbxpb1n5cd8j2fh", "depends": ["BiocFileCache", "EBImage", "HDF5Array", "Matrix", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "TENxIO", "arrow", "dplyr", "ggplot2", "shiny"] }, "xmapbridge": { "name": "xmapbridge", "version": "1.66.0", "sha256": "1vhvagfpicc35vp25hrf9v56rlqz5yzb4zg5jr01yx1vrz3fikgj", "depends": [] }, "yamss": { "name": "yamss", "version": "1.34.1", "sha256": "0ap2qdxidqryx0793gfsd0wzjrfvck6fdgk2588y8ccvi8y72j0c", "depends": ["BiocGenerics", "EBImage", "IRanges", "Matrix", "S4Vectors", "SummarizedExperiment", "data_table", "limma", "mzR"] }, "yarn": { "name": "yarn", "version": "1.34.0", "sha256": "1a73jnyz1961kk35s64wb5iz4asbvm59lkhdhvg6r310xb3yp1sz", "depends": ["Biobase", "RColorBrewer", "biomaRt", "downloader", "edgeR", "gplots", "limma", "matrixStats", "preprocessCore", "quantro", "readr"] }, "zFPKM": { "name": "zFPKM", "version": "1.30.0", "sha256": "1ydh535r6x3r6ad0xxnn0iwq1v77xg8ik851gxqy6hnl6gscs1zb", "depends": ["SummarizedExperiment", "checkmate", "dplyr", "ggplot2", "tidyr"] }, "zellkonverter": { "name": "zellkonverter", "version": "1.18.0", "sha256": "0w221y7mcn6i53lqrkvs00jl315z18hvvxrylg9rlvzmca9ac3ri", "depends": ["DelayedArray", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "basilisk", "cli", "reticulate"] }, "zenith": { "name": "zenith", "version": "1.10.0", "sha256": "0na9fx9h8a5c8h7fp8lm9pb6basdwz6y7gqq4bi2yfbpyk0k8dz4", "depends": ["EnrichmentBrowser", "GSEABase", "Rdpack", "Rfast", "dplyr", "ggplot2", "limma", "msigdbr", "progress", "reshape2", "tidyr", "variancePartition"] }, "zinbwave": { "name": "zinbwave", "version": "1.30.0", "sha256": "02rzf371kp7gkklw4yq08mmxkfj7fha2jc7qm00m1d3kwqancljj", "depends": ["BiocParallel", "Matrix", "SingleCellExperiment", "SummarizedExperiment", "edgeR", "genefilter", "softImpute"] }, "zitools": { "name": "zitools", "version": "1.2.0", "sha256": "1wb4k0c4xxar3ncklvj96b41x15yj90jwbvrmlbqd559bhhqych3", "depends": ["BiocGenerics", "DESeq2", "MatrixGenerics", "RColorBrewer", "SummarizedExperiment", "VGAM", "dplyr", "ggplot2", "magrittr", "matrixStats", "phyloseq", "pscl", "reshape2", "tibble", "tidyr"] }, "zlibbioc": { "name": "zlibbioc", "version": "1.54.0", "sha256": "0ll3v5b9yk63rqiwm4g0dwan22mqkj2lv1b6czwghbpl1jpv2jrd", "depends": [] }, "ABAEnrichment": { "name": "ABAEnrichment", "version": "1.2.2", "sha256": "0hmxxp12w67lp1g1djzlxffwlx32mnd1wbmz1hmv7y7z6h6ichvq", "depends": ["ABAData", "Rcpp", "gplots"], "broken": true }, "ALPS": { "name": "ALPS", "version": "1.5.0", "sha256": "1aydvzc6x0871iasij68xqdlhjyg69qbqxm0qh1q52w8gj2nyq3p", "depends": ["assertthat", "BiocParallel", "ChIPseeker", "corrplot", "data_table", "dplyr", "genefilter", "GenomicRanges", "GGally", "gghalves", "ggplot2", "ggseqlogo", "Gviz", "magrittr", "org_Hs_eg_db", "plyr", "reshape2", "rtracklayer", "stringr", "tibble", "tidyr", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene"], "broken": true }, "ASpediaFI": { "name": "ASpediaFI", "version": "1.11.0", "sha256": "13jny6ca8hdf269z37baaggfs7jss00ln09apn42pj411g3p7nms", "depends": ["BiocParallel", "biomaRt", "dplyr", "DRaWR", "e1071", "fgsea", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "Gviz", "igraph", "IRanges", "IVAS", "limma", "Matrix", "reshape2", "ROCR", "Rsamtools", "rtracklayer", "S4Vectors", "scales", "SummarizedExperiment"], "broken": true }, "ATACCoGAPS": { "name": "ATACCoGAPS", "version": "1.6.0", "sha256": "09h32q9y7z65ck33rwqzw2wkl8l6016s0sdkhf2g094yxhkz26rh", "depends": ["BSgenome_Hsapiens_UCSC_hg19", "BSgenome_Mmusculus_UCSC_mm10", "CoGAPS", "GeneOverlap", "GenomicFeatures", "GenomicRanges", "Homo_sapiens", "IRanges", "JASPAR2016", "Mus_musculus", "TFBSTools", "chromVAR", "dplyr", "fgsea", "gplots", "gtools", "motifmatchr", "msigdbr", "projectR", "rGREAT", "stringr", "tidyverse"], "broken": true }, "AffyCompatible": { "name": "AffyCompatible", "version": "1.30.0", "sha256": "1qw741j4d9b7bczjz3s72a9d0dcxbh5a2raak3ggwmz72p53axfz", "depends": ["Biostrings", "RCurl", "XML"], "broken": true }, "AffyExpress": { "name": "AffyExpress", "version": "1.36.0", "sha256": "186gc8c3bj070zvwyy4vz44wx1r85bbmil78b6m9kvwp6q1856d7", "depends": ["affy", "limma"], "broken": true }, "AffyTiling": { "name": "AffyTiling", "version": "1.28.0", "sha256": "08n1w64yk1pxb9d8dpa86y3mqxrsvyq0gsfzlsqg6fz8jz497fhr", "depends": ["affxparser", "affy", "preprocessCore"], "broken": true }, "AnalysisPageServer": { "name": "AnalysisPageServer", "version": "1.4.1", "sha256": "0zq0h9abswvhkpgb6f966rhgj7lh02aykq88fphxfv9zzkjfxbjp", "depends": ["Biobase", "graph", "log4r", "rjson"], "broken": true }, "AnnotationFuncs": { "name": "AnnotationFuncs", "version": "1.20.0", "sha256": "03rznpbsgq3pdh0id35vp8984f57ws2jpb0cww1qxglf967gy028", "depends": ["AnnotationDbi"], "broken": true }, "ArrayExpressHTS": { "name": "ArrayExpressHTS", "version": "1.20.0", "sha256": "00a5h3nwwhi9phrys2gj0ba8a24iqxk09licb0jn1qzdz9mrfxmq", "depends": ["Biobase", "BiocGenerics", "Biostrings", "DESeq", "GenomicRanges", "Hmisc", "IRanges", "R2HTML", "RColorBrewer", "Rsamtools", "ShortRead", "XML", "biomaRt", "bitops", "edgeR", "rJava", "sampling", "sendmailR", "snow", "svMisc"], "broken": true }, "ArrayTV": { "name": "ArrayTV", "version": "1.8.0", "sha256": "0ny5x2w0n3di5wzywfngsfdxaciczs24cnbvk75mv6hf4bdwfp74", "depends": ["DNAcopy", "foreach", "oligoClasses"], "broken": true }, "ArrayTools": { "name": "ArrayTools", "version": "1.30.0", "sha256": "168llqk8w1b54xy0ijg0m8mzcwggawkdr4s7abi2fv4q5007s1jv", "depends": ["Biobase", "affy", "limma", "xtable"], "broken": true }, "AtlasRDF": { "name": "AtlasRDF", "version": "1.6.0", "sha256": "16hgw47px7ig6hrm90y5nzy3dgdfm5my58bli20aj6dhnh2yvhxd", "depends": ["hash"], "broken": true }, "Autotuner": { "name": "Autotuner", "version": "1.7.0", "sha256": "0k07gs6bnxs0894iqi1lhk96mifjcdf68bv4q9fjv50nzqpzqd8l", "depends": ["assertthat", "Biobase", "cluster", "entropy", "MSnbase", "mzR", "RColorBrewer", "scales"], "broken": true }, "BAC": { "name": "BAC", "version": "1.30.0", "sha256": "1yrw01m8fd54v352pcb7904f8wi3il83nx8ywf6m968x33y2npxn", "depends": [], "broken": true }, "BDMMAcorrect": { "name": "BDMMAcorrect", "version": "1.18.1", "sha256": "17lsgl5mczfk2flkrclxhsqkkpr6mncccywm68l0z02pi5xhd8j7", "depends": ["ape", "ellipse", "ggplot2", "Rcpp", "RcppArmadillo", "RcppEigen", "SummarizedExperiment", "vegan"], "broken": true }, "BEARscc": { "name": "BEARscc", "version": "1.24.0", "sha256": "0f66pbhf4fz66021k7f6rlwzxdikznbhjqqpxwrj07yg65q5sd1l", "depends": ["SingleCellExperiment", "data_table", "ggplot2"], "broken": true }, "BGmix": { "name": "BGmix", "version": "1.30.0", "sha256": "1ii0cvqpz7ai779r4hx8yimsx69ln1f7qlw7jvp3k606z52kqkp2", "depends": ["KernSmooth"], "broken": true }, "BHC": { "name": "BHC", "version": "1.22.0", "sha256": "0m8w4b3ihnmvccy32nwvgzwn7k9i018ydw8iz19b6kz5r5c89q17", "depends": [], "broken": true }, "BRGenomics": { "name": "BRGenomics", "version": "1.14.1", "sha256": "09kpb9jn84np1z8k72ngsbd0xx6v0x3kcl738wizr64w0j9zhlla", "depends": ["DESeq2", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "rtracklayer", "S4Vectors", "SummarizedExperiment"], "broken": true }, "BayesPeak": { "name": "BayesPeak", "version": "1.22.0", "sha256": "1jmn8p461rmgjarf4rlhyqzrjg8xkpq56rlrk6964kqxp6jkh8bi", "depends": ["IRanges"], "broken": true }, "BioMM": { "name": "BioMM", "version": "1.15.0", "sha256": "01lfw0npcclcyqqh2xkhjq9jw0irbk13fsj5y1b3rz1amzzngg6p", "depends": ["BiocParallel", "CMplot", "e1071", "ggplot2", "glmnet", "imager", "lattice", "nsprcomp", "precrec", "ranger", "rms", "topGO", "vioplot", "xlsx"], "broken": true }, "BioNetStat": { "name": "BioNetStat", "version": "1.22.0", "sha256": "1rbb36v64b9xbk2dsf6wsyrhwwbkysrj8fp1g22y3gisdk170sg8", "depends": ["BiocParallel", "DT", "ggplot2", "Hmisc", "igraph", "knitr", "markdown", "pathview", "pheatmap", "plyr", "psych", "RColorBrewer", "RJSONIO", "rmarkdown", "shiny", "shinyBS", "whisker", "yaml"], "broken": true }, "BioPlex": { "name": "BioPlex", "version": "1.2.3", "sha256": "0cn0x6ij2a3xy61bq0qy5amp0ipj4r4shh7g0vlwbkrclj9w347r", "depends": ["BiocFileCache", "GenomeInfoDb", "GenomicRanges", "GEOquery", "graph", "SummarizedExperiment"], "broken": true }, "BioSeqClass": { "name": "BioSeqClass", "version": "1.28.0", "sha256": "0pv63d57hck04dpha20pzyzz7przzvi536nmgnsig5zw16lis4f2", "depends": ["Biobase", "Biostrings", "class", "e1071", "foreign", "ipred", "klaR", "nnet", "party", "randomForest", "rpart", "scatterplot3d", "tree"], "broken": true }, "BiocCaseStudies": { "name": "BiocCaseStudies", "version": "1.32.0", "sha256": "0wn3a01l6d62prrncmy22dx4nqsgzq3lw24ybf676ghrmjaygmyc", "depends": ["Biobase"], "broken": true }, "BiocDockerManager": { "name": "BiocDockerManager", "version": "1.11.0", "sha256": "0w393f14i253pnk0jzf2ci4g5cnxshwdjmix2r8arlnadh7spjyk", "depends": ["dplyr", "httr", "memoise", "readr", "whisker"], "broken": true }, "BiocInstaller": { "name": "BiocInstaller", "version": "1.20.3", "sha256": "0hjfhzbpxr7sfxac46ihklq0l7gkglrp7qi48vcp1s7xapnikblr", "depends": [], "broken": true }, "BiocOncoTK": { "name": "BiocOncoTK", "version": "1.24.0", "sha256": "0h4cr7lrmbyx7kdj81s7ff75svr01rvzn54svqi93vjilawmpbm3", "depends": ["ComplexHeatmap", "DBI", "DT", "GenomicFeatures", "GenomicRanges", "IRanges", "MASS", "Rgraphviz", "S4Vectors", "SummarizedExperiment", "bigrquery", "car", "curatedTCGAData", "dplyr", "ggplot2", "ggpubr", "graph", "httr", "magrittr", "plyr", "rjson", "scales", "shiny"], "broken": true }, "BitSeq": { "name": "BitSeq", "version": "1.14.0", "sha256": "1q58za8jd96bk2wxy7np0b7lar3v0pk6ll833k10x1b260rvpgbp", "depends": ["IRanges", "Rsamtools", "S4Vectors", "zlibbioc"], "broken": true }, "BrainSABER": { "name": "BrainSABER", "version": "1.8.0", "sha256": "1nxcjvaip7pp387bhdc2pmjai3chib1n63ig0cslhppzzjp2y6jd", "depends": ["BiocFileCache", "biomaRt", "data_table", "lsa", "S4Vectors", "shiny", "SummarizedExperiment"], "broken": true }, "BrainStars": { "name": "BrainStars", "version": "1.14.0", "sha256": "0r6jd6h48c15sg655079lwr9v1gl79wk8773w2q9fyfmakhj15vx", "depends": ["Biobase", "RCurl", "RJSONIO"], "broken": true }, "BrowserVizDemo": { "name": "BrowserVizDemo", "version": "1.2.3", "sha256": "1pj9b0nhkrc3bcs36dpm2hy9lsfp2xwnrlf99b9v6n96ijki8bg9", "depends": ["BiocGenerics", "BrowserViz", "httpuv", "jsonlite"], "broken": true }, "CALIB": { "name": "CALIB", "version": "1.36.0", "sha256": "1b21f0zg4czhk4pbd3c3vbl0p4qpw0l4wg17lm1gw4b6d6ml7jsb", "depends": ["limma"], "broken": true }, "CAnD": { "name": "CAnD", "version": "1.2.1", "sha256": "0ncpa81ac6dzkhqnr56i4nzzipsmzy44n71z6sdhpa39rgdar2a7", "depends": ["ggplot2", "reshape"], "broken": true }, "CBEA": { "name": "CBEA", "version": "1.6.0", "sha256": "1mbd62wakjn9pwhy2q2hfxkx09ny577a4j6lssnjj65jb3s7gjr6", "depends": ["BiocParallel", "BiocSet", "Rcpp", "SummarizedExperiment", "TreeSummarizedExperiment", "dplyr", "fitdistrplus", "generics", "glue", "goftest", "lmom", "magrittr", "mixtools", "rlang", "tibble", "tidyr"], "broken": true }, "CNPBayes": { "name": "CNPBayes", "version": "1.0.0", "sha256": "06jw9xi0q5slh1xghgj1js5bn1gsmpag0w84cxa7qf5ls1bw4xp6", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "Rcpp", "S4Vectors", "combinat", "foreach", "gtools", "matrixStats", "oligoClasses"], "broken": true }, "CNVgears": { "name": "CNVgears", "version": "1.8.0", "sha256": "1p7dxzkna3czkpsidj586hfwhymrjwvjr6q5f2pq7zlmpn6f8svx", "depends": ["data_table", "ggplot2"], "broken": true }, "CNVtools": { "name": "CNVtools", "version": "1.64.0", "sha256": "1sm28sl7ghcfrgjd0d741zfy21r6vxkhj8cn510z95aa49icpd8j", "depends": ["survival"], "broken": true }, "COHCAP": { "name": "COHCAP", "version": "1.8.0", "sha256": "1lak57k8b8jcd21wajr1ivi1sml73fsvb6jbdz6nxgjbq7al1hgk", "depends": ["COHCAPanno", "WriteXLS"], "broken": true }, "CORREP": { "name": "CORREP", "version": "1.36.0", "sha256": "0hjkwl2mf173mfdrziiadf5hacz6j67skizch44rxc2kfj7sbhyb", "depends": ["e1071"], "broken": true }, "CSSP": { "name": "CSSP", "version": "1.8.0", "sha256": "05x0agbcpns8s3vmbs7ygdny249vcahzk7sqv50nz39ap2c7i309", "depends": [], "broken": true }, "CancerInSilico": { "name": "CancerInSilico", "version": "2.18.0", "sha256": "0szbz88wnr3dbf7k9bhihv6hkr29gsp9vrllr201wx5qfzl2gncy", "depends": ["BH", "Rcpp"], "broken": true }, "CancerMutationAnalysis": { "name": "CancerMutationAnalysis", "version": "1.13.0", "sha256": "0c3yjscd1jlgfl869vnv37qdb0y5gicnja1why9ws95qqgmij6zl", "depends": ["AnnotationDbi", "limma", "qvalue"], "broken": true }, "CancerSubtypes": { "name": "CancerSubtypes", "version": "1.26.0", "sha256": "06lw7b43fwh554870w71i676q6gm6kx53580cgg17a7prdjndkmr", "depends": ["cluster", "ConsensusClusterPlus", "impute", "limma", "NMF", "sigclust", "survival"], "broken": true }, "CellaRepertorium": { "name": "CellaRepertorium", "version": "1.12.0", "sha256": "0k9sxh0b9g2841zpkbmcc65v0kfyv1i6sxzdmbr49nzzm27xlbh2", "depends": ["BiocGenerics", "Biostrings", "dplyr", "forcats", "generics", "glue", "Matrix", "progress", "purrr", "Rcpp", "reshape2", "rlang", "S4Vectors", "stringr", "tibble", "tidyr"], "broken": true }, "ChIC": { "name": "ChIC", "version": "1.19.0", "sha256": "0zbmhixxn3skn8csz93fyyfamz1n3gzjzb2caw8ybi2cysgzz5ys", "depends": ["BiocGenerics", "caret", "caTools", "ChIC_data", "genomeIntervals", "GenomicRanges", "IRanges", "progress", "randomForest", "Rsamtools", "S4Vectors"], "broken": true }, "Clonality": { "name": "Clonality", "version": "1.18.0", "sha256": "0rx3k8c55q831dhfh5dpkl3px8jj6glx6i3la80r9krx68mbp947", "depends": ["DNAcopy"], "broken": true }, "CoRegNet": { "name": "CoRegNet", "version": "1.6.0", "sha256": "0ynizawrygpka2isldbfmnlz1zqczx2fv1kbvz1lbm9qwbpj7rn4", "depends": ["arules", "igraph", "shiny"], "broken": true }, "CompGO": { "name": "CompGO", "version": "1.6.0", "sha256": "0n84z3mhg6zb3yafz0803g6cggzpbw31fn933q9bg7pybij0nf1p", "depends": ["GenomicFeatures", "RDAVIDWebService", "Rgraphviz", "TxDb_Mmusculus_UCSC_mm9_knownGene", "ggplot2", "pathview", "pcaMethods", "reshape2", "rtracklayer"], "broken": true }, "CopyNumber450k": { "name": "CopyNumber450k", "version": "1.6.0", "sha256": "0z4v6x140gzaxf06a73d2qd6dp8gvq62l8xb7bii21r7n089m14i", "depends": ["Biobase", "BiocGenerics", "DNAcopy", "minfi", "preprocessCore"], "broken": true }, "CopywriteR": { "name": "CopywriteR", "version": "2.2.0", "sha256": "0hmww433hyg4wgi2hx49mwrd4y65myyi00akys3mhdsxn3s0al13", "depends": ["BiocParallel", "CopyhelpeR", "DNAcopy", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "chipseq", "data_table", "futile_logger", "gtools", "matrixStats"], "broken": true }, "CorMut": { "name": "CorMut", "version": "1.12.0", "sha256": "0ldqw4g15i4r1nv74msn97c75wcr1nvwk1ffnkafvnc8bwcfzfmy", "depends": ["igraph", "seqinr"], "broken": true }, "CountClust": { "name": "CountClust", "version": "1.21.0", "sha256": "17px9jkpjwz0j2f5h8xv52wh24ilqvlb6dvczjc36lb7mq4cw3sq", "depends": ["cowplot", "flexmix", "ggplot2", "gtools", "limma", "maptpx", "picante", "plyr", "reshape2", "slam", "SQUAREM"], "broken": true }, "CytoTree": { "name": "CytoTree", "version": "1.6.0", "sha256": "1dsdhwjkd3ngnw50fs6vz048afk47r95vhi0wqj8sip11nhndkd8", "depends": ["Biobase", "BiocNeighbors", "cluster", "destiny", "flowCore", "FlowSOM", "flowUtils", "ggplot2", "gmodels", "igraph", "limma", "Matrix", "matrixStats", "mclust", "pheatmap", "prettydoc", "RANN", "Rcpp", "Rtsne", "scatterpie", "scatterplot3d", "stringr", "sva", "umap"], "broken": true }, "DASiR": { "name": "DASiR", "version": "1.10.0", "sha256": "1by2655qvskzynvbh47vydm6nl2cmnfqqs25453k29n672a6yyw4", "depends": ["Biostrings", "GenomicRanges", "IRanges", "XML"], "broken": true }, "DAVIDQuery": { "name": "DAVIDQuery", "version": "1.29.0", "sha256": "0gvm6qjx8y61nbnbz66md74pfc4awj4900pjr8q1m5sip5yzbxj2", "depends": ["RCurl"], "broken": true }, "DBChIP": { "name": "DBChIP", "version": "1.14.0", "sha256": "1x876cv2j0bdb7jflm663bp7xk32rsxpf9jwwskbl8r4r1ffsapa", "depends": ["DESeq", "edgeR"], "broken": true }, "DChIPRep": { "name": "DChIPRep", "version": "1.0.4", "sha256": "0cwggkpbza25r2yssyhs9zkwzncmxkd406k2sn2y0rq1kdi08hj2", "depends": ["DESeq2", "GenomicRanges", "S4Vectors", "assertthat", "fdrtool", "ggplot2", "plyr", "reshape2", "smoothmest", "tidyr"], "broken": true }, "DEComplexDisease": { "name": "DEComplexDisease", "version": "1.18.0", "sha256": "12gw9b0gdwyih51j2gzay6vxhycgc52n8svd0slv6wsbw5rc19lh", "depends": ["BiocParallel", "ComplexHeatmap", "DESeq2", "edgeR", "Rcpp", "SummarizedExperiment"], "broken": true }, "DEDS": { "name": "DEDS", "version": "1.44.0", "sha256": "079c3in183ybp0c46hqh99grqmbshsnrcax3qz08z5xbc394azna", "depends": [], "broken": true }, "DESeq": { "name": "DESeq", "version": "1.22.1", "sha256": "14rc1zcn4a7hkm43ca9js5ffhcm3awjrpl5bx66fj3szibjnnzcb", "depends": ["Biobase", "BiocGenerics", "MASS", "RColorBrewer", "genefilter", "geneplotter", "lattice", "locfit"], "broken": true }, "DIAlignR": { "name": "DIAlignR", "version": "2.12.0", "sha256": "19zgjnd9sjxx09pcf50fl3w4fmd1gj8g765x114l0cqcpk9qfmm5", "depends": ["DBI", "RMSNumpress", "RSQLite", "Rcpp", "RcppEigen", "ape", "bit64", "data_table", "dplyr", "ggplot2", "magrittr", "mzR", "phangorn", "pracma", "reticulate", "rlang", "signal", "tidyr", "zoo"], "broken": true }, "DMRforPairs": { "name": "DMRforPairs", "version": "1.6.0", "sha256": "0b5mkhb5gkvfccvpgvklb3ksnq9gv6napcvxzcrph46nmm11i8zc", "depends": ["GenomicRanges", "Gviz", "R2HTML"], "broken": true }, "DOQTL": { "name": "DOQTL", "version": "1.6.0", "sha256": "0sl7a1hhszrfxn52iw7cz6sl38y7mwk4giw3a7kqj22f1p6bhc6y", "depends": ["BSgenome_Mmusculus_UCSC_mm10", "Biobase", "BiocGenerics", "GenomicRanges", "IRanges", "QTLRel", "RUnit", "Rsamtools", "VariantAnnotation", "XML", "annotate", "annotationTools", "biomaRt", "corpcor", "doParallel", "foreach", "fpc", "hwriter", "iterators", "mclust", "regress", "rhdf5"], "broken": true }, "DeProViR": { "name": "DeProViR", "version": "1.0.0", "sha256": "0m1nhzq5kl6jyi3d8fzb77iplzc4p85v7lj5q7i7125kjv6bycsm", "depends": ["BiocFileCache", "PRROC", "caret", "data_table", "dplyr", "fmsb", "ggplot2", "keras", "pROC", "readr"], "broken": true }, "DeepBlueR": { "name": "DeepBlueR", "version": "1.27.0", "sha256": "03v1ag250zq8wj3fxnsg2ii8l93vq6dg9dxqyiqdjnbvxc0y26xg", "depends": ["data_table", "diffr", "dplyr", "filehash", "foreach", "GenomeInfoDb", "GenomicRanges", "R_utils", "RCurl", "rjson", "rtracklayer", "settings", "stringr", "withr", "XML"], "broken": true }, "DupChecker": { "name": "DupChecker", "version": "1.8.0", "sha256": "0p75kq178mls765q2v22bj7a727hb1v5rj4wkcagxavcls92vg0p", "depends": ["RCurl", "R_utils"], "broken": true }, "EBSeqHMM": { "name": "EBSeqHMM", "version": "1.4.0", "sha256": "02ba8famhbp4nxkg8jkwzs63qkfi7hi03h6w1igl2xn2343fnla3", "depends": ["EBSeq"], "broken": true }, "EDDA": { "name": "EDDA", "version": "1.8.0", "sha256": "0gqgq57a11k7iygjyf3bszx8gm90a8frabmzib7kk84k3wrvynqg", "depends": ["DESeq", "ROCR", "Rcpp", "baySeq", "edgeR", "snow"], "broken": true }, "ELBOW": { "name": "ELBOW", "version": "1.6.0", "sha256": "1kpprsv1s08qks10raqdh82c9w8dg0saxa1ahhnk1a2whzxj0n3m", "depends": [], "broken": true }, "ENCODExplorer": { "name": "ENCODExplorer", "version": "1.2.4", "sha256": "0vx4q628g0h1wdcp4hibs44h8avnyin0ccxijrdk94s5n2f91pc2", "depends": ["RSQLite", "jsonlite"], "broken": true }, "ENVISIONQuery": { "name": "ENVISIONQuery", "version": "1.18.0", "sha256": "1fyp6qyvw5cbapnpjx1s86pss2xhv98s4lqxfxwrsng6p1jh5z89", "depends": ["XML", "rJava"], "broken": true }, "EasyqpcR": { "name": "EasyqpcR", "version": "1.12.0", "sha256": "0s0ir8bpj3fwg79mzqz57c0crkqqq7hywiwyihcz2cykhsm1r11g", "depends": ["matrixStats", "plotrix", "plyr"], "broken": true }, "ExpressionView": { "name": "ExpressionView", "version": "1.22.0", "sha256": "1gwhz8q5kyi01jwlwpd39dp292pc6k4v1w0al4653151qb5m55ja", "depends": ["AnnotationDbi", "GO_db", "KEGG_db", "bitops", "caTools", "eisa", "isa2"], "broken": true }, "FCBF": { "name": "FCBF", "version": "2.8.0", "sha256": "1clg3s2av70j0pm0yj0ckvlklkkg5zb0r057pz6wmklllfkmx1dv", "depends": ["ggplot2", "gridExtra", "mclust", "pbapply", "SummarizedExperiment"], "broken": true }, "FEM": { "name": "FEM", "version": "2.6.0", "sha256": "1pwbn2igwrd50wn8402f3zwd22h4c8anjmbrls2i6h86ardl046f", "depends": ["AnnotationDbi", "BiocGenerics", "Matrix", "corrplot", "graph", "igraph", "impute", "limma", "marray", "org_Hs_eg_db"], "broken": true }, "FScanR": { "name": "FScanR", "version": "1.10.0", "sha256": "1v4iq2wlvxf0wbs2d9ip3pcfx3a533pqp4as9pr0f6q57cvqi2bs", "depends": [], "broken": true }, "FindMyFriends": { "name": "FindMyFriends", "version": "1.0.7", "sha256": "0ga0iwscbcczysldizgp8g19gsyszfw4vgbgs45q9px95603z0cg", "depends": ["Biobase", "BiocParallel", "Biostrings", "IRanges", "Matrix", "Rcpp", "S4Vectors", "digest", "dplyr", "filehash", "ggdendro", "ggplot2", "gtable", "igraph", "kebabs", "reshape2"], "broken": true }, "FlowRepositoryR": { "name": "FlowRepositoryR", "version": "1.2.0", "sha256": "1y1y7g9111z55cwi2ph44yqib41234g77xwsybk6irlq1anizz7p", "depends": ["RCurl", "XML"], "broken": true }, "FoldGO": { "name": "FoldGO", "version": "1.18.0", "sha256": "0h08yv1kykllaanc562ncwv3ajic7cd4wcqba24nlbh6agsazwyk", "depends": ["ggplot2", "tidyr", "topGO"], "broken": true }, "FourCSeq": { "name": "FourCSeq", "version": "1.4.0", "sha256": "1xh0l90hp6jy9j0xkh78dm9kyk90zzlg04yfrzd4v12mwljs8r19", "depends": ["Biobase", "Biostrings", "DESeq2", "GenomicAlignments", "GenomicRanges", "LSD", "Matrix", "Rsamtools", "SummarizedExperiment", "fda", "ggbio", "ggplot2", "gtools", "reshape2", "rtracklayer"], "broken": true }, "FunChIP": { "name": "FunChIP", "version": "1.28.0", "sha256": "1qhwabm7vgjqmgxdla6qs70sncvzjc8qh5vpq5xqp50hk1lli7f1", "depends": ["doParallel", "fda", "foreach", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "RColorBrewer", "Rcpp", "Rsamtools", "shiny"], "broken": true }, "FunciSNP": { "name": "FunciSNP", "version": "1.12.0", "sha256": "1125ismkp2sprshv4b39l6bycdlry3933jaliva17c0bgjr27jhm", "depends": ["AnnotationDbi", "ChIPpeakAnno", "FunciSNP_data", "GenomicRanges", "IRanges", "Rsamtools", "TxDb_Hsapiens_UCSC_hg19_knownGene", "VariantAnnotation", "ggplot2", "org_Hs_eg_db", "plyr", "reshape", "rtracklayer", "scales", "snpStats"], "broken": true }, "GAPGOM": { "name": "GAPGOM", "version": "1.11.0", "sha256": "0sl97w5zx4zdrdbcwayqyvgxspaxpbils3mpsrim0zlspjrjcy6z", "depends": ["AnnotationDbi", "Biobase", "BiocFileCache", "data_table", "dplyr", "fastmatch", "GEOquery", "GO_db", "GOSemSim", "graph", "igraph", "magrittr", "Matrix", "matrixStats", "org_Hs_eg_db", "org_Mm_eg_db", "plyr", "RBGL"], "broken": true }, "GCSConnection": { "name": "GCSConnection", "version": "1.7.0", "sha256": "1psmw3825whyzvbzqpqksgcl09b6kfyb8k5vny6ljkjbac1jzvnf", "depends": ["googleAuthR", "googleCloudStorageR", "httr", "jsonlite", "Rcpp"], "broken": true }, "GCSFilesystem": { "name": "GCSFilesystem", "version": "1.6.0", "sha256": "0qk8xyg06f71y4r1q1zpcj89irh9i6cd9z6nqlx635x8if84sh6d", "depends": [], "broken": true }, "GCSscore": { "name": "GCSscore", "version": "1.14.0", "sha256": "0fqr0sgplpbkdpvwgi8fpmwmnqja41622pvkkzsalbzai021hgp3", "depends": ["affxparser", "Biobase", "BiocManager", "data_table", "devtools", "dplR", "RSQLite", "stringr"], "broken": true }, "GENE_E": { "name": "GENE.E", "version": "1.10.0", "sha256": "1czm1j144i842d7lf01c9gmyifikp4a66sq49i7rgpzbiz3pndkf", "depends": ["RCurl", "rhdf5"], "broken": true }, "GEOsearch": { "name": "GEOsearch", "version": "1.0.1", "sha256": "1zag3rg2cfs0zfh092rzwhshnkncrv2p88flz9hy2n350k1xnyc4", "depends": ["org_Hs_eg_db", "org_Mm_eg_db"], "broken": true }, "GGBase": { "name": "GGBase", "version": "3.32.0", "sha256": "15vvwigv9xy87dl2c795c3abpnrzr364m4sbslmns403rg8dpsiw", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "GenomicRanges", "IRanges", "Matrix", "S4Vectors", "SummarizedExperiment", "digest", "genefilter", "limma", "snpStats"], "broken": true }, "GGtools": { "name": "GGtools", "version": "5.6.0", "sha256": "1ndvlyfzjn519z9zh6kf5sdjaz3ckracgyf2lxp23nchm2311lf0", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "Biostrings", "GGBase", "GenomeInfoDb", "GenomicRanges", "Gviz", "IRanges", "ROCR", "Rsamtools", "S4Vectors", "VariantAnnotation", "biglm", "bit", "data_table", "ff", "ggplot2", "hexbin", "iterators", "reshape2", "rtracklayer", "snpStats"], "broken": true }, "GISPA": { "name": "GISPA", "version": "1.26.0", "sha256": "19vbcfdf959xs6kgds37ij3qay9x61dzrlvcs238m7hywl4dn3lz", "depends": ["Biobase", "changepoint", "data_table", "genefilter", "GSEABase", "HH", "lattice", "latticeExtra", "plyr", "scatterplot3d"], "broken": true }, "GOFunction": { "name": "GOFunction", "version": "1.18.0", "sha256": "00pdxf24sxdnh31h69c5zjhl1j2jv1ag91ay3a9w62p07bcg82l6", "depends": ["AnnotationDbi", "Biobase", "GO_db", "Rgraphviz", "SparseM", "graph"], "broken": true }, "GOSim": { "name": "GOSim", "version": "1.8.0", "sha256": "14dyazr7p9p7h1cckbmd5yjj76718lqgfnqbcrrz52qyk0dqz6wx", "depends": ["AnnotationDbi", "GO_db", "Matrix", "RBGL", "Rcpp", "annotate", "cluster", "corpcor", "flexmix", "graph", "org_Hs_eg_db", "topGO"], "broken": true }, "GOsummaries": { "name": "GOsummaries", "version": "2.4.7", "sha256": "0kl77jqd2bdbp8v2rrjp21j265r05fnagpz8jwj8m9scgrd5hwh4", "depends": ["Rcpp", "gProfileR", "ggplot2", "gtable", "limma", "plyr", "reshape2"], "broken": true }, "GRridge": { "name": "GRridge", "version": "1.22.0", "sha256": "0vmwm50dwk3im3qx40vh9ipmfqywzz5fmmm79b74zjcd3qjrznf3", "depends": ["glmnet", "graph", "Iso", "mvtnorm", "penalized", "survival"], "broken": true }, "GeneAccord": { "name": "GeneAccord", "version": "1.15.0", "sha256": "1dlnqdcrl1fv5yf0zwfgkqfd2x19fv6q84p7c730nmnnaqal6md1", "depends": ["biomaRt", "caTools", "dplyr", "ggplot2", "ggpubr", "gtools", "magrittr", "maxLik", "RColorBrewer", "reshape2", "tibble"], "broken": true }, "GeneAnswers": { "name": "GeneAnswers", "version": "2.12.0", "sha256": "1gacvc1vd0sl6jn0r14w4n37hsrmx6m5k1l7d2a5m3qssyk6l6n3", "depends": ["Biobase", "Heatplus", "MASS", "RBGL", "RColorBrewer", "RCurl", "RSQLite", "XML", "annotate", "downloader", "igraph"], "broken": true }, "GeneSelector": { "name": "GeneSelector", "version": "2.20.0", "sha256": "179mjqk9w4zm33mhja7hmwphpnxsv32mh60avs2mqmq9fi9z6pdh", "depends": ["Biobase", "limma", "multtest", "samr", "siggenes"], "broken": true }, "GeneticsDesign": { "name": "GeneticsDesign", "version": "1.38.0", "sha256": "1yh8s40fr0yqbch7ix9y4p22ih0008xpjy5nn5x37y575l41hhwh", "depends": ["gmodels", "gtools", "mvtnorm"], "broken": true }, "GenoGAM": { "name": "GenoGAM", "version": "2.11.0", "sha256": "058qix2h0zm2k9csmbdhci2wqih3lyggjj591cqn0ls2nv7bnyvj", "depends": ["BiocParallel", "Biostrings", "data_table", "DelayedArray", "DESeq2", "futile_logger", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "HDF5Array", "IRanges", "Matrix", "Rcpp", "RcppArmadillo", "rhdf5", "Rsamtools", "S4Vectors", "sparseinv", "SummarizedExperiment"], "broken": true }, "GenoView": { "name": "GenoView", "version": "1.3.0", "sha256": "09k9xjmx3qmsfr3a4vrfgs73r0xsymf5m4gl0zjjk4cnfk7bs41v", "depends": ["GenomicRanges", "biovizBase", "ggbio", "ggplot2", "gridExtra"], "broken": true }, "GenomeGraphs": { "name": "GenomeGraphs", "version": "1.30.0", "sha256": "1wkjcg6w95wlrdgaskc3xndl0azmxhxnsipf9qrj057gf2rpx7zf", "depends": ["biomaRt"], "broken": true }, "Genominator": { "name": "Genominator", "version": "1.24.0", "sha256": "1rqzxbji5wh6dshjsprj1mzps08l07gxmjir9naj6lsj2q0xhn9p", "depends": ["BiocGenerics", "DBI", "GenomeGraphs", "IRanges", "RSQLite"], "broken": true }, "GoogleGenomics": { "name": "GoogleGenomics", "version": "1.2.0", "sha256": "1z87jmd5vzg5v93bv9k3998wqhnk5p2v9d2qr9g0xxjvxw2q78fm", "depends": ["Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "VariantAnnotation", "httr", "rjson"], "broken": true }, "GraphPAC": { "name": "GraphPAC", "version": "1.12.1", "sha256": "1fa64jam3cl1khv8jspwjb9myifmgx0kwg0b601bia578bjcdj7d", "depends": ["RMallow", "TSP", "iPAC", "igraph"], "broken": true }, "HCsnip": { "name": "HCsnip", "version": "1.10.0", "sha256": "0x4lpx13bhr2w5yhrcsc89g0x4q1dy0j588h210ziizgh67qqcrs", "depends": ["Biobase", "clusterRepro", "coin", "fpc", "impute", "randomForestSRC", "sigaR", "sm", "survival"], "broken": true }, "HPAStainR": { "name": "HPAStainR", "version": "1.9.0", "sha256": "1bjysi3x8248f262v4rzi2y50rlzryb987wbvdjy6af84nq7hd09", "depends": ["data_table", "dplyr", "scales", "shiny", "stringr", "tibble", "tidyr"], "broken": true }, "HTSanalyzeR": { "name": "HTSanalyzeR", "version": "2.22.0", "sha256": "01mb273v1i9k0d2gbl9mpmr4rrnx49s3srv0yh1znvmwx0hmfyq2", "depends": ["AnnotationDbi", "BioNet", "GSEABase", "RankProd", "biomaRt", "cellHTS2", "graph", "igraph"], "broken": true }, "HTSeqGenie": { "name": "HTSeqGenie", "version": "3.20.1", "sha256": "0bg86jiv45899gw9x4hhvqf525vfwkzj2b5jk7026cq5vmjc0k5j", "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "Cairo", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "ShortRead", "VariantAnnotation", "VariantTools", "chipseq", "gmapR", "hwriter", "rtracklayer"], "broken": true }, "HumanTranscriptomeCompendium": { "name": "HumanTranscriptomeCompendium", "version": "1.20.0", "sha256": "1y46zsl08k6sdih8psar85fyc5dfk2vraxmfry70zx57vbjbin92", "depends": ["BiocManager", "S4Vectors", "SummarizedExperiment", "shiny", "ssrch"], "broken": true }, "IPPD": { "name": "IPPD", "version": "1.18.0", "sha256": "1kl4rx6rdmpkm7bd2w8ncvz4sb8x6wljvxkif2l17yflsp1wjvp2", "depends": ["MASS", "Matrix", "XML", "bitops", "digest"], "broken": true }, "IRISFGM": { "name": "IRISFGM", "version": "1.8.0", "sha256": "1n13rsbg5y0xnr6in18silifx8jhqzjj1vb5kpjgy5ml55im1s5r", "depends": ["AdaptGauss", "AnnotationDbi", "anocva", "clusterProfiler", "colorspace", "DEsingle", "DrImpute", "ggplot2", "ggpubr", "ggraph", "igraph", "knitr", "Matrix", "MCL", "mixtools", "org_Hs_eg_db", "org_Mm_eg_db", "pheatmap", "Polychrome", "RColorBrewer", "Rcpp", "scater", "scran", "Seurat", "SingleCellExperiment"], "broken": true }, "IdMappingAnalysis": { "name": "IdMappingAnalysis", "version": "1.14.0", "sha256": "11rn1b6665b64h3a4mb8qkg5kp5l9ha6aa14f512k7lzs1vcczpm", "depends": ["Biobase", "RColorBrewer", "R_oo", "boot", "mclust", "rChoiceDialogs"], "broken": true }, "IdMappingRetrieval": { "name": "IdMappingRetrieval", "version": "1.18.2", "sha256": "0wl2ybv23z84rlq2szk46kvcdm0bmqy0mjga9n33wz1c04br2bxj", "depends": ["AffyCompatible", "ENVISIONQuery", "RCurl", "R_methodsS3", "R_oo", "XML", "biomaRt", "rChoiceDialogs"], "broken": true }, "Imetagene": { "name": "Imetagene", "version": "1.0.0", "sha256": "1di9nx5ad0wd17byn740azx9yb6hd12dzvlfl8s5iyas4z9qzwya", "depends": ["ggplot2", "metagene", "shiny", "shinyBS", "shinyFiles", "shinythemes"], "broken": true }, "ImmuneSpaceR": { "name": "ImmuneSpaceR", "version": "1.30.0", "sha256": "0lhilrh4xyw1cvqnx4b6g0llm9b1i4l2r476d4hmypkkgl25q8n7", "depends": ["Biobase", "curl", "data_table", "digest", "flowCore", "flowWorkspace", "ggplot2", "gplots", "heatmaply", "httr", "jsonlite", "pheatmap", "plotly", "preprocessCore", "R6", "Rlabkey", "rmarkdown", "scales"], "broken": true }, "IntOMICS": { "name": "IntOMICS", "version": "1.2.0", "sha256": "1qhni8p8zap9szi499jrdxkacdrb7vdd4va5h4n0kdi4qr80vrzh", "depends": ["bestNormalize", "bnlearn", "bnstruct", "cowplot", "ggplot2", "ggraph", "gplots", "igraph", "matrixStats", "numbers", "RColorBrewer", "rlang", "SummarizedExperiment"], "broken": true }, "InterMineR": { "name": "InterMineR", "version": "1.26.0", "sha256": "0isw4rg89139xmrcfb9r7jc3z8jj1my4radhinah0vad2cwb36l0", "depends": ["Biostrings", "GenomicRanges", "IRanges", "RCurl", "RJSONIO", "S4Vectors", "SummarizedExperiment", "XML", "httr", "igraph", "sqldf", "xml2"], "broken": true }, "IsoGeneGUI": { "name": "IsoGeneGUI", "version": "2.6.0", "sha256": "1b7my9ri3kwi4rbdymcnwdjzv88pgdfjf2ax4gls0v4460hwg5az", "depends": ["Biobase", "Iso", "ORCME", "ORIClust", "RColorBrewer", "Rcpp", "ff", "geneplotter", "goric", "jpeg", "multtest", "relimp", "tkrplot", "xlsx"], "broken": true }, "KEGGprofile": { "name": "KEGGprofile", "version": "1.12.0", "sha256": "08yg0vn7d0yyamwj8s9bg9130y1dag34w5j9dhi00x7381jnrxwr", "depends": ["AnnotationDbi", "KEGGREST", "KEGG_db", "TeachingDemos", "XML", "biomaRt", "png"], "broken": true }, "LMGene": { "name": "LMGene", "version": "2.26.0", "sha256": "0mfs8kpirwkv8salg6aacy0hr0zwmmxr7pzh88sxj3x71k2dclzi", "depends": ["Biobase", "affy", "multtest", "survival"], "broken": true }, "LPEadj": { "name": "LPEadj", "version": "1.30.0", "sha256": "0ll9n3wkaink16laj2y98hb0kx5dglz776zlwdfkw54l1fjvvj5h", "depends": ["LPE"], "broken": true }, "LVSmiRNA": { "name": "LVSmiRNA", "version": "1.20.0", "sha256": "1q43harvk7q5wb8yjffhvzs4dxl8h5vp60ngym5vcvapxr8iym3w", "depends": ["Biobase", "BiocGenerics", "MASS", "SparseM", "affy", "limma", "quantreg", "vsn", "zlibbioc"], "broken": true }, "LineagePulse": { "name": "LineagePulse", "version": "1.21.0", "sha256": "09x1i7slysqf3dpjzck6rgfzhyswaj0kk8i047yscg8fcaksbmqg", "depends": ["BiocParallel", "circlize", "ComplexHeatmap", "ggplot2", "gplots", "knitr", "Matrix", "RColorBrewer", "SingleCellExperiment", "SummarizedExperiment"], "broken": true }, "LowMACA": { "name": "LowMACA", "version": "1.2.0", "sha256": "12jm8psg7rnrsxydcqzfgiryy6lk5mxyximfzn7hnqqvxbs3wc55", "depends": ["BiocParallel", "Biostrings", "LowMACAAnnotation", "RColorBrewer", "data_table", "motifStack", "reshape2", "stringr"], "broken": true }, "M3D": { "name": "M3D", "version": "1.4.0", "sha256": "088ghd9r5jr51179cj9hbk1dpj4f9fkrbgyghlq29w2bbgzc57xx", "depends": ["BiSeq", "GenomicRanges", "IRanges"], "broken": true }, "MACPET": { "name": "MACPET", "version": "1.15.1", "sha256": "0742i3fxg2793lhgpxb4whh6mwvzd4bn86ykd0rv8sgilxyq5zsl", "depends": ["BH", "bigmemory", "BiocParallel", "Biostrings", "futile_logger", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "GEOquery", "gtools", "InteractionSet", "intervals", "IRanges", "knitr", "plyr", "Rbowtie", "Rcpp", "Rsamtools", "rtracklayer", "S4Vectors", "ShortRead"], "broken": true }, "MAGeCKFlute": { "name": "MAGeCKFlute", "version": "2.9.0", "sha256": "1m2yq73q9wwv5kfybgnkdb877dy539x9vpx713pr6xjpkqvksfiv", "depends": ["Biobase", "DOSE", "clusterProfiler", "depmap", "enrichplot", "ggplot2", "ggrepel", "gridExtra", "msigdbr", "pathview", "reshape2"], "broken": true }, "MCRestimate": { "name": "MCRestimate", "version": "2.26.0", "sha256": "1igfffsgz6m4rl2a5fnkb92r5x4qjr2yl8gaj3ws8478q3aq0bgd", "depends": ["Biobase", "RColorBrewer", "e1071", "golubEsets", "pamr", "randomForest"], "broken": true }, "MIGSA": { "name": "MIGSA", "version": "1.21.0", "sha256": "0b7w9lzi8xb1vzh7zahw7wh9jm7x1y04rs2gvvjmfbdfw085rdpm", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocParallel", "data_table", "edgeR", "futile_logger", "ggdendro", "ggplot2", "GO_db", "GOstats", "graph", "GSEABase", "ismev", "jsonlite", "limma", "matrixStats", "org_Hs_eg_db", "RBGL", "reshape2", "Rgraphviz", "vegan"], "broken": true }, "MIMOSA": { "name": "MIMOSA", "version": "1.8.1", "sha256": "1mkxp83gwxw581gz13vb8lbl2pff7al75lhjcvwxv6gxb1k272xi", "depends": ["Biobase", "Formula", "MASS", "MCMCpack", "Rcpp", "RcppArmadillo", "coda", "data_table", "ggplot2", "modeest", "plyr", "pracma", "reshape", "scales", "testthat"], "broken": true }, "MMAPPR2": { "name": "MMAPPR2", "version": "1.14.0", "sha256": "14m41hi79f7m2qigjjcgy08awrf0654ridgm6wxcq8cmmlm68g8a", "depends": ["Biobase", "BiocGenerics", "BiocParallel", "data_table", "dplyr", "ensemblVEP", "GenomeInfoDb", "GenomicRanges", "gmapR", "IRanges", "magrittr", "Rsamtools", "S4Vectors", "stringr", "tidyr", "VariantAnnotation", "VariantTools"], "broken": true }, "MMDiff": { "name": "MMDiff", "version": "1.10.0", "sha256": "0v000a87ciw83xj6p2443k1zs1w98ax38nzaf643wqmb8szwr6vf", "depends": ["Biobase", "DiffBind", "GenomicRanges", "IRanges", "Rsamtools"], "broken": true }, "MQmetrics": { "name": "MQmetrics", "version": "1.10.0", "sha256": "15jkmdj2k5h8vbi332y7b4xzm2330g2s13l6lf2d1v9pg5aqrisq", "depends": ["cowplot", "dplyr", "ggforce", "gghalves", "ggplot2", "ggpubr", "ggrepel", "gridExtra", "gtable", "knitr", "magrittr", "plyr", "purrr", "RColorBrewer", "readr", "reshape2", "rlang", "rmarkdown", "scales", "stringr", "tidyr"], "broken": true }, "MSEADbi": { "name": "MSEADbi", "version": "1.2.0", "sha256": "1g1kg3nh7iwg5nrpmig6srw6as4yfwmbqn965pffrk0zp19llsbf", "depends": ["AnnotationDbi", "Biobase", "DBI", "RSQLite"], "broken": true }, "MSGFgui": { "name": "MSGFgui", "version": "1.4.0", "sha256": "0pb9i81pqnz05jrwqh9myz5zchdn8ng5nrsv3cmdg4713yskqpcw", "depends": ["MSGFplus", "mzID", "mzR", "shiny", "shinyFiles", "xlsx"], "broken": true }, "MSGFplus": { "name": "MSGFplus", "version": "1.4.0", "sha256": "1hw40kyhkxm0iy60n3y1cw2k52q5vjl47k4z5x34syq5d14iplva", "depends": ["mzID"], "broken": true }, "MSstatsSampleSize": { "name": "MSstatsSampleSize", "version": "1.13.0", "sha256": "09gmlqxb65pa4wxh5bryb6lhs68zrfaqfl7n3k9shvzi3iw02vp3", "depends": ["BiocParallel", "caret", "ggplot2", "gridExtra", "MSstats", "reshape2"], "broken": true }, "MSstatsTMTPTM": { "name": "MSstatsTMTPTM", "version": "1.1.2", "sha256": "16qnddwhwhjjfr5akdrmp93gkxq2r41s82hb1blbz47lwbj5kaj5", "depends": ["dplyr", "ggplot2", "gridExtra", "MSstatsTMT", "Rcpp", "reshape2", "stringr"], "broken": true }, "MeSHSim": { "name": "MeSHSim", "version": "1.2.0", "sha256": "1wgc2s1080sm2dn9ny4c1kpbcmbv4gv91h7jmgya9p8lk224aasr", "depends": ["RCurl", "XML"], "broken": true }, "MergeMaid": { "name": "MergeMaid", "version": "2.42.0", "sha256": "1ajmrcpvzfjk0bkm2v3yklry91w5cxpjhgjr9hfszzldfhh5sfw4", "depends": ["Biobase", "MASS", "survival"], "broken": true }, "MetaVolcanoR": { "name": "MetaVolcanoR", "version": "1.14.0", "sha256": "11fxjv0kb65wc2237rh3340j72v3zsd4s019bi07rbpqnl246pnj", "depends": ["cowplot", "data_table", "dplyr", "ggplot2", "htmlwidgets", "metafor", "metap", "plotly", "rlang", "tidyr", "topconfects"], "broken": true }, "Metab": { "name": "Metab", "version": "1.4.1", "sha256": "0wi45k7lx7f7y8bfpa4d1lggnkxlwwyjgzw22xyfw9yj40ma5x9g", "depends": ["pander", "svDialogs", "xcms"], "broken": true }, "MethCP": { "name": "MethCP", "version": "1.11.0", "sha256": "099jaadjfalvxpwq3k630yrqa1dfbp8rqn2fahz1rsha3y5z9bys", "depends": ["BiocParallel", "bsseq", "DNAcopy", "DSS", "GenomeInfoDb", "GenomicRanges", "IRanges", "methylKit", "S4Vectors"], "broken": true }, "Mirsynergy": { "name": "Mirsynergy", "version": "1.6.0", "sha256": "0wb257fi5wygky6iqaxdhp8n3pxzknv1vy44ay55y0bal1nbkzwa", "depends": ["Matrix", "RColorBrewer", "ggplot2", "gridExtra", "igraph", "reshape", "scales"], "broken": true }, "MmPalateMiRNA": { "name": "MmPalateMiRNA", "version": "1.20.0", "sha256": "1salsb4askcv6xgzfwcwxkrr8qx7pjzqgljbw3ips2f4n6vqvyzj", "depends": ["Biobase", "lattice", "limma", "statmod", "vsn", "xtable"], "broken": true }, "MoPS": { "name": "MoPS", "version": "1.4.0", "sha256": "07bylvhv1wnzj3z2ycw4rb29mlz34sbpksl0sdk47q9f5cjgvlnf", "depends": ["Biobase"], "broken": true }, "MobilityTransformR": { "name": "MobilityTransformR", "version": "1.6.0", "sha256": "1292fk08zi1zf0hdj56vzdgv9h9nr16vmbzypqkam7lvqqnig49h", "depends": ["MetaboCoreUtils", "MSnbase", "Spectra", "xcms"], "broken": true }, "MotIV": { "name": "MotIV", "version": "1.26.0", "sha256": "0s26dklw8kav8lz0245as7y9znj4yfiknpmcgrdmm62rq04c11mp", "depends": ["BiocGenerics", "Biostrings", "IRanges", "S4Vectors", "lattice", "rGADEM"], "broken": true }, "NBSplice": { "name": "NBSplice", "version": "1.15.0", "sha256": "0yn7s7igshall34cflmdwvmknv8h1zdi6vg8svvcyn9fvzlgjdm8", "depends": ["BiocParallel", "car", "edgeR", "ggplot2", "MASS", "reshape2"], "broken": true }, "NGScopy": { "name": "NGScopy", "version": "1.4.0", "sha256": "1vs7mi0lb8jcm9yc0jz7rvdnj95fr06cf1jkb9p84pnm9vpn63d6", "depends": ["changepoint"], "broken": true }, "NanoStringQCPro": { "name": "NanoStringQCPro", "version": "1.2.0", "sha256": "1cbja0bi4sw3n4f1wkgbvmwh1hr49hhrybqxc6a7f8lvq11s28rf", "depends": ["AnnotationDbi", "Biobase", "NMF", "RColorBrewer", "knitr", "org_Hs_eg_db", "png"], "broken": true }, "NarrowPeaks": { "name": "NarrowPeaks", "version": "1.14.0", "sha256": "08nhw2ira3amjs9zl134afjqwi0hniq0g3mgmljjp1l0277b8acg", "depends": ["BiocGenerics", "CSAR", "GenomeInfoDb", "GenomicRanges", "ICSNP", "IRanges", "S4Vectors", "fda"], "broken": true }, "NeighborNet": { "name": "NeighborNet", "version": "1.18.0", "sha256": "046k1799wz77ww4jhf935pfz2637dmzy7p848iyjxj1yc5g51jq8", "depends": ["graph"], "broken": true }, "NeuCA": { "name": "NeuCA", "version": "1.10.0", "sha256": "0k5bqdrja3x238fyrd7dm5jm94igh25b0ipb2zj6scpa4m15n67l", "depends": ["SingleCellExperiment", "e1071", "kableExtra", "keras", "limma"], "broken": true }, "NxtIRFcore": { "name": "NxtIRFcore", "version": "1.6.0", "sha256": "1x3645v6ar8mpmyk6hd5w3m38496g68l2vdh80vh0hhlqlrp17n2", "depends": ["AnnotationHub", "BiocFileCache", "BiocGenerics", "BiocParallel", "Biostrings", "BSgenome", "data_table", "DelayedArray", "DelayedMatrixStats", "fst", "genefilter", "GenomeInfoDb", "GenomicRanges", "ggplot2", "HDF5Array", "IRanges", "magrittr", "NxtIRFdata", "plotly", "R_utils", "Rcpp", "RcppProgress", "rhdf5", "rtracklayer", "S4Vectors", "SummarizedExperiment", "zlibbioc"], "broken": true }, "ODER": { "name": "ODER", "version": "1.6.0", "sha256": "17c3hvdghli6i88yqy6dclzyad60s0d6y4hng6i4bycc9fnan41w", "depends": ["BiocFileCache", "BiocGenerics", "dasper", "data_table", "derfinder", "dplyr", "GenomeInfoDb", "GenomicRanges", "ggplot2", "ggpubr", "ggrepel", "IRanges", "magrittr", "megadepth", "plyr", "purrr", "rtracklayer", "S4Vectors", "stringr", "tibble"], "broken": true }, "OGSA": { "name": "OGSA", "version": "1.0.0", "sha256": "058lfd60w905jvhq99dsdcvl1q6h9dnwhqdqn942yr54jlkc7fjy", "depends": ["Biobase", "gplots", "limma"], "broken": true }, "OmicsLonDA": { "name": "OmicsLonDA", "version": "1.15.0", "sha256": "1kn26k0lnk7hgfzk1kh5bh41zkia8a4pzsfr35mbjrflcxmvgk2w", "depends": ["BiocGenerics", "BiocParallel", "ggplot2", "gss", "plyr", "pracma", "SummarizedExperiment", "zoo"], "broken": true }, "OmicsMarkeR": { "name": "OmicsMarkeR", "version": "1.2.0", "sha256": "1r4qn2p5fxyi6r9l7zgbga1n5wcy18whcvyx0cwrr7lawbzjn6yg", "depends": ["caTools", "caret", "data_table", "e1071", "foreach", "gbm", "glmnet", "pamr", "permute", "plyr", "randomForest"], "broken": true }, "OperaMate": { "name": "OperaMate", "version": "1.2.3", "sha256": "1zgqf2ywazrxc66l2x8280izrzanan51b8vz5jwy8i7gnrm4gaa0", "depends": ["fBasics", "gProfileR", "ggplot2", "gridExtra", "pheatmap", "reshape2", "stabledist"], "broken": true }, "OutlierD": { "name": "OutlierD", "version": "1.34.0", "sha256": "19wrakxv833r5jqcrk627kgn6pissna9xdfnhn389a0j50xb02is", "depends": ["Biobase", "quantreg"], "broken": true }, "PAPi": { "name": "PAPi", "version": "1.10.0", "sha256": "0q90yi4s3jln713cpylgan7fzw7c536kw7bqlnkkaw6rjj1k6vvg", "depends": ["KEGGREST", "svDialogs"], "broken": true }, "PAnnBuilder": { "name": "PAnnBuilder", "version": "1.34.0", "sha256": "086hgqx9svn1pfzcz6affj2p9kvjk5k4viqkmwknlk9smw53l40l", "depends": ["AnnotationDbi", "Biobase", "DBI", "RSQLite"], "broken": true }, "PCpheno": { "name": "PCpheno", "version": "1.32.0", "sha256": "023dkbi3r1bs9wiihx3rcdc1dx5w21pfmk0n3n7zan4k5jkz4rwx", "depends": ["AnnotationDbi", "Biobase", "Category", "GO_db", "GSEABase", "KEGG_db", "SLGI", "ScISI", "annotate", "graph", "ppiData", "ppiStats"], "broken": true }, "PERFect": { "name": "PERFect", "version": "1.14.0", "sha256": "0ygbirfnp122c8jzrig5cnm6rxyhz126ixl5ca49i13kizcv2ns9", "depends": ["fitdistrplus", "ggplot2", "Matrix", "phyloseq", "psych", "sn", "zoo"], "broken": true }, "PFP": { "name": "PFP", "version": "1.7.0", "sha256": "1328a73ggg7l1drjbmv67jcvlv83khn1k252mf81xj4gf213d0di", "depends": ["clusterProfiler", "ggplot2", "graph", "igraph", "KEGGgraph", "magrittr", "plyr", "tidyr"], "broken": true }, "PGA": { "name": "PGA", "version": "1.0.0", "sha256": "1s4ddjlnxh1waw1sm428lnaq655qfzlmabcjgdm95fi2cg66vs86", "depends": ["AnnotationDbi", "Biostrings", "GenomicFeatures", "GenomicRanges", "IRanges", "Nozzle_R1", "RCurl", "RSQLite", "Rsamtools", "VariantAnnotation", "biomaRt", "customProDB", "data_table", "ggplot2", "pheatmap", "rTANDEM", "rtracklayer", "stringr"], "broken": true }, "PGSEA": { "name": "PGSEA", "version": "1.44.0", "sha256": "0cfz479nlmbal4bs5ah12q6jpp7989xic59rml87i19bcbhz8z26", "depends": ["AnnotationDbi", "Biobase", "GO_db", "KEGG_db", "annaffy"], "broken": true }, "PSEA": { "name": "PSEA", "version": "1.4.0", "sha256": "1df2v472s2g4qcylvg9y5gahgjzq0m753j65736c8lc7g2zbpacp", "depends": ["Biobase", "MASS"], "broken": true }, "PSICQUIC": { "name": "PSICQUIC", "version": "1.8.3", "sha256": "1g3xkbgr3by0gd8ngiavxyy14ixdhrwcf5ka329k3129d816425p", "depends": ["BiocGenerics", "IRanges", "RCurl", "biomaRt", "httr", "plyr"], "broken": true }, "PanViz": { "name": "PanViz", "version": "1.6.0", "sha256": "1h4fxqxkaph5j3vkfhmmkhvmqa8czzdzxcg6f06v94hqf38i86i5", "depends": ["RColorBrewer", "colorspace", "data_table", "dplyr", "easycsv", "futile_logger", "igraph", "magrittr", "rentrez", "rlang", "stringr", "tibble", "tidyr"], "broken": true }, "PanVizGenerator": { "name": "PanVizGenerator", "version": "1.22.0", "sha256": "0rhx2jc5kc9bl00v16frh8b4075n0jqn4s37pkvqp3ypcbqws32d", "depends": ["igraph", "jsonlite", "pcaMethods", "shiny"], "broken": true }, "Pbase": { "name": "Pbase", "version": "0.10.0", "sha256": "02b2vw63gwssy6bz8v6dvfmz2ak5pa7wzz341nrbr3mwv0k27j4q", "depends": ["Biobase", "BiocGenerics", "Biostrings", "GenomicRanges", "Gviz", "IRanges", "MSnbase", "Pviz", "Rcpp", "S4Vectors", "biomaRt", "cleaver", "mzID", "mzR", "rtracklayer"], "broken": true }, "Pi": { "name": "Pi", "version": "2.14.0", "sha256": "16jh7p3f6nk2hwvp44b9sas1dl618m520xj553x9dkaj77jmzp6d", "depends": ["BiocGenerics", "caret", "dplyr", "GenomeInfoDb", "GenomicRanges", "ggnetwork", "ggplot2", "ggrepel", "glmnet", "igraph", "IRanges", "lattice", "MASS", "Matrix", "osfr", "plot3D", "purrr", "randomForest", "RCircos", "readr", "ROCR", "scales", "supraHex", "tibble", "tidyr"], "broken": true }, "PloGO2": { "name": "PloGO2", "version": "1.14.0", "sha256": "0r0zf8dfb4pv4hv5fp5v61i3q5bnzwxws1v3cnx7l64b0hjl2ffi", "depends": ["GO_db", "GOstats", "httr", "lattice", "openxlsx", "xtable"], "broken": true }, "PoTRA": { "name": "PoTRA", "version": "1.13.0", "sha256": "1a32d1wndb24pxza3h53yddj9z2clff5srny2k00pbbfq1h99mjf", "depends": ["BiocGenerics", "graph", "graphite", "igraph", "org_Hs_eg_db"], "broken": true }, "Polyfit": { "name": "Polyfit", "version": "1.4.0", "sha256": "0rhs81hclz59nqirpp9y5n7qmg343s260n1gv8ma3c8j2jicb333", "depends": ["DESeq"], "broken": true }, "PrecisionTrialDrawer": { "name": "PrecisionTrialDrawer", "version": "1.11.0", "sha256": "1miw8rj1zn1xv97dkgs66k9g21i6gp3j2m1l1akysskczgam3i2c", "depends": ["BiocParallel", "biomaRt", "brglm", "data_table", "DT", "GenomicRanges", "ggplot2", "ggrepel", "googleVis", "httr", "IRanges", "jsonlite", "LowMACAAnnotation", "magrittr", "matrixStats", "RColorBrewer", "reshape2", "S4Vectors", "shiny", "shinyBS", "stringr", "XML"], "broken": true }, "Prize": { "name": "Prize", "version": "1.0.0", "sha256": "1a9hvhpa29ns7lhzmdqjlasp6rwrzng8klaw9cz54vdvc7al49wn", "depends": ["diagram", "ggplot2", "gplots", "matrixcalc", "reshape2", "stringr"], "broken": true }, "ProCoNA": { "name": "ProCoNA", "version": "1.8.0", "sha256": "0j0ld484cd98304fncyixi86qnxh72m8s83xxyk8c81kf7lzvhw1", "depends": ["BiocGenerics", "GOstats", "MSnbase", "WGCNA", "flashClust"], "broken": true }, "ProteomicsAnnotationHubData": { "name": "ProteomicsAnnotationHubData", "version": "1.0.1", "sha256": "1wxx6mq1xs7l24p82rs0wsmfxhrjx6nv1m7wf73i33vrcy83g2i6", "depends": ["AnnotationHub", "AnnotationHubData", "Biobase", "BiocInstaller", "Biostrings", "GenomeInfoDb", "MSnbase", "RCurl", "mzR"], "broken": true }, "PubScore": { "name": "PubScore", "version": "1.8.0", "sha256": "18bmzvv6mxrdlh297i29q24vi5rc4x2mjaryi5asiki186x0hy8d", "depends": ["dplyr", "ggplot2", "ggrepel", "igraph", "intergraph", "network", "progress", "rentrez", "sna"], "broken": true }, "QUALIFIER": { "name": "QUALIFIER", "version": "1.14.1", "sha256": "1h87y2q8x4ri6sv7nbppzpqa96m99mijq1739h8cfab5wmi0bcl5", "depends": ["Biobase", "MASS", "XML", "data_table", "flowCore", "flowViz", "flowWorkspace", "hwriter", "lattice", "latticeExtra", "ncdfFlow", "reshape"], "broken": true }, "QuartPAC": { "name": "QuartPAC", "version": "1.2.0", "sha256": "0nx3a9jsp2rq61jszm6kgpbqi9m5jkqfvk94npp7nk3qwhfi00j8", "depends": ["GraphPAC", "SpacePAC", "data_table", "iPAC"], "broken": true }, "RCytoscape": { "name": "RCytoscape", "version": "1.20.1", "sha256": "1ymbj8xlny9bsbcxyvg9si7v2rlc7bw3sq0424bsfc92l3as0rjj", "depends": ["BiocGenerics", "graph"], "broken": true }, "RDAVIDWebService": { "name": "RDAVIDWebService", "version": "1.8.0", "sha256": "1f92a80zksp90wlj2iymdf20hqkbp1aw7mdb7w5r19zckskcrg1m", "depends": ["Category", "GO_db", "GOstats", "RBGL", "ggplot2", "graph", "rJava"], "broken": true }, "RGMQL": { "name": "RGMQL", "version": "1.24.0", "sha256": "1p7s17i18ql3b8yvg6pmcz62ql18ncd3hqk0rganmahfbd91idby", "depends": ["BiocGenerics", "GenomicRanges", "RGMQLlib", "S4Vectors", "data_table", "dplyr", "glue", "httr", "plyr", "rJava", "rtracklayer", "xml2"], "broken": true }, "RGalaxy": { "name": "RGalaxy", "version": "1.14.0", "sha256": "1g63kmfywmnjammifjkqiy8cnqvb77d2x4yff8bgz2ib60gyqm14", "depends": ["Biobase", "BiocGenerics", "XML", "digest", "optparse", "roxygen2"], "broken": true }, "RIPAT": { "name": "RIPAT", "version": "1.10.0", "sha256": "154a79xyihxkg3sbwxz9ch0ixqlqv9gwkpsv88i55c75qyzkx2sm", "depends": ["biomaRt", "GenomicRanges", "ggplot2", "IRanges", "karyoploteR", "openxlsx", "plyr", "regioneR", "rtracklayer", "stringr"], "broken": true }, "RIPSeeker": { "name": "RIPSeeker", "version": "1.10.0", "sha256": "09pr25pf488vdim3k6mvbvqqyxhl2dfs4y699x8xyhym34c74xcj", "depends": ["GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "SummarizedExperiment", "rtracklayer"], "broken": true }, "RLSeq": { "name": "RLSeq", "version": "1.5.2", "sha256": "0nhip321gbv6phwdwi3qkbmhnfh7fhb9md6xs4lklskwkkrd7s1q", "depends": ["AnnotationHub", "aws_s3", "callr", "caretEnsemble", "circlize", "ComplexHeatmap", "dplyr", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "ggplot2", "ggplotify", "ggprism", "pheatmap", "RColorBrewer", "regioneR", "rtracklayer", "valr", "VennDiagram"], "broken": true }, "RNASeqR": { "name": "RNASeqR", "version": "1.16.0", "sha256": "0m7d3mm644n81630v2m6vv7798x3rjshb9jcp63xq631j1wmk63i", "depends": ["ballgown", "Biostrings", "clusterProfiler", "corrplot", "DESeq2", "DOSE", "edgeR", "factoextra", "FactoMineR", "ggplot2", "gridExtra", "org_Hs_eg_db", "org_Sc_sgd_db", "pathview", "PerformanceAnalytics", "pheatmap", "rafalib", "reshape2", "reticulate", "Rsamtools", "stringr", "systemPipeR", "systemPipeRdata"], "broken": true }, "RNAinteract": { "name": "RNAinteract", "version": "1.18.0", "sha256": "0v7hz20nsc2dkb4xjzdhib2rj8k9zkn2c71rhg46b6hy3jxrm7m1", "depends": ["Biobase", "ICS", "ICSNP", "RColorBrewer", "abind", "cellHTS2", "geneplotter", "gplots", "hwriter", "lattice", "latticeExtra", "limma", "locfit", "splots"], "broken": true }, "RNAither": { "name": "RNAither", "version": "2.18.7", "sha256": "1mgm6y5ijlw3rpfi0vkdlw0zrfd4ciz3qmmp42vykmm8c5jsjc0x", "depends": ["RankProd", "biomaRt", "car", "geneplotter", "limma", "prada", "splots", "topGO"], "broken": true }, "RNAprobR": { "name": "RNAprobR", "version": "1.2.0", "sha256": "017sc7ba5kw55rc74acv3i5i0mg7h5hblaqxy4j2ln6iqm1h38fi", "depends": ["BiocGenerics", "Biostrings", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Rsamtools", "plyr", "rtracklayer"], "broken": true }, "RWebServices": { "name": "RWebServices", "version": "1.34.0", "sha256": "05czankzfvgsfrs2am8dkglzcix22s7gc4bgci0a66x8z31dlkx0", "depends": ["RCurl", "SJava", "TypeInfo"], "broken": true }, "RamiGO": { "name": "RamiGO", "version": "1.16.0", "sha256": "12mwfcljw323aqpzc4z5hl2h5qy51bpi5z59x4hx8inw3vc3n55y", "depends": ["RCurl", "RCytoscape", "graph", "gsubfn", "igraph", "png"], "broken": true }, "RandomWalkRestartMH": { "name": "RandomWalkRestartMH", "version": "1.22.0", "sha256": "0mvh22p0dliwapdgbl5r93dpjdfnvnxdv5ig3y9gd2ndn32h1cyc", "depends": ["igraph", "Matrix"], "broken": true }, "Rariant": { "name": "Rariant", "version": "1.6.2", "sha256": "1jf8p5i6jqlniwrmsk6ajcrf6j637cx267nvb2742yd1jzfm5yy3", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "SomaticSignatures", "VGAM", "VariantAnnotation", "dplyr", "exomeCopy", "ggbio", "ggplot2", "reshape2", "shiny"], "broken": true }, "Rcade": { "name": "Rcade", "version": "1.12.0", "sha256": "08q62agkyb810b0hfvs9vb9rh0ls8zrz83558xprijjizrkg9cg2", "depends": ["GenomicRanges", "Rsamtools", "S4Vectors", "baySeq", "plotrix", "rgl"], "broken": true }, "Rchemcpp": { "name": "Rchemcpp", "version": "2.8.0", "sha256": "0zz9s3zvxgs6mpiq085zy20sqajyx1645cz3848h2l0w1w5m6lga", "depends": ["ChemmineR", "Rcpp"], "broken": true }, "RchyOptimyx": { "name": "RchyOptimyx", "version": "2.10.0", "sha256": "0cmyjyr3dn8df9ss4zhhm6y1lhf68msl5br070x01i8kgh4dagky", "depends": ["Rgraphviz", "flowType", "graph", "sfsmisc"], "broken": true }, "ReQON": { "name": "ReQON", "version": "1.16.0", "sha256": "1j79vmhk34argysbjyxcsmfjsplkxq4cn8gprm6min1v08xzryg0", "depends": ["Rsamtools", "rJava", "seqbias"], "broken": true }, "ReactomeContentService4R": { "name": "ReactomeContentService4R", "version": "1.12.0", "sha256": "1qqrkki9v3ggwqv88n7w3wp50y4gxvkixrg1sad23vl08jd0rkl6", "depends": ["data_table", "doParallel", "foreach", "httr", "jsonlite", "magick"], "broken": true }, "ReactomeGraph4R": { "name": "ReactomeGraph4R", "version": "1.12.0", "sha256": "17xkrqyp5wdsdd0gpplsk3qfsr8sgf1ap0vz6v34xlhbmzdq3rs8", "depends": ["ReactomeContentService4R", "data_table", "doParallel", "foreach", "getPass", "jsonlite", "magrittr", "neo4r", "purrr", "rlang"], "broken": true }, "RefNet": { "name": "RefNet", "version": "1.6.1", "sha256": "0l0krjjk1jld7z5zy6k3z6m2qkqd86yj92xfck75q3bq3jm96h0j", "depends": ["AnnotationHub", "BiocGenerics", "IRanges", "PSICQUIC", "RCurl", "shiny"], "broken": true }, "RefPlus": { "name": "RefPlus", "version": "1.40.0", "sha256": "13qlm4smaafx1x78wn959wc1rm4wns7l6qgdmh1lg5khkrrh3x19", "depends": ["Biobase", "affy", "affyPLM", "preprocessCore"], "broken": true }, "Rgin": { "name": "Rgin", "version": "1.15.0", "sha256": "1x5zj2d5rvsr2xh0ifpnrys9v91dal1xxhv5mmk16rs8wzwqpqba", "depends": ["RcppEigen"], "broken": true }, "Ringo": { "name": "Ringo", "version": "1.34.0", "sha256": "0r549n840sq9whaz8nk7rz3wardxc8jvwdni4bd5f7zzrhj0ynhl", "depends": ["Biobase", "BiocGenerics", "Matrix", "RColorBrewer", "genefilter", "lattice", "limma", "vsn"], "broken": true }, "Risa": { "name": "Risa", "version": "1.12.0", "sha256": "0s23fbdk1v1cg0c67vhkz53wava1swjig8fz8jsv8av0pqb0rg17", "depends": ["Biobase", "Rcpp", "affy", "biocViews", "xcms"], "broken": true }, "RmiR": { "name": "RmiR", "version": "1.26.0", "sha256": "1nnpr5jp5anbqbgyg53qqjhi49bibymc0l3yj6ar5d6csavrympb", "depends": ["DBI", "RmiR_Hs_miRNA"], "broken": true }, "Roleswitch": { "name": "Roleswitch", "version": "1.8.0", "sha256": "0libkpp9scrbakhzp030bx86f4np6ijn01r8xzn02f5106h23gz7", "depends": ["Biobase", "Biostrings", "DBI", "biomaRt", "microRNA", "plotrix", "pracma", "reshape"], "broken": true }, "Rolexa": { "name": "Rolexa", "version": "1.26.0", "sha256": "184v27zycmqnj4fpjgrxl3vcxxfxwkbfqdzm6wsyxixm93rmz7v4", "depends": ["Biostrings", "IRanges", "ShortRead", "mclust"], "broken": true }, "RpsiXML": { "name": "RpsiXML", "version": "2.12.0", "sha256": "0zlcr1f5sf98bwxakbmq33kniwlpxcc32z5fz7vqsasyv5vbz1ks", "depends": ["AnnotationDbi", "Biobase", "RBGL", "XML", "annotate", "graph", "hypergraph"], "broken": true }, "SAGx": { "name": "SAGx", "version": "1.44.0", "sha256": "0rrw1y80ybpskwvcdbyqq8m4d17sz07bv9gpa27rvfq2sy4znsk6", "depends": ["Biobase", "multtest"], "broken": true }, "SCATE": { "name": "SCATE", "version": "1.10.0", "sha256": "1fkswn9xlbr4mrnr62yzk51dri7rzbvf28whh7qhdfxgyvavw439", "depends": ["GenomicAlignments", "GenomicRanges", "mclust", "preprocessCore", "Rtsne", "SCATEData", "splines2", "xgboost"], "broken": true }, "SEPA": { "name": "SEPA", "version": "1.0.0", "sha256": "1hvkz3pyp8qkq1mjw9wl426db6n3ay05bx2djkdpvpbai4fjwgvc", "depends": ["ggplot2", "org_Hs_eg_db", "org_Mm_eg_db", "reshape2", "segmented", "shiny", "topGO"], "broken": true }, "SEPIRA": { "name": "SEPIRA", "version": "1.20.0", "sha256": "1yhlm6l9jv8fhdhnhpj7r8cdpnrp1la287x85gcssqjnv5v4k047", "depends": ["corpcor", "limma"], "broken": true }, "SISPA": { "name": "SISPA", "version": "1.0.0", "sha256": "01kf83hlc7qyyxr4dx86m9vc16cydrkw4sajs2ikpn2fnrqkx6z1", "depends": ["GSVA", "changepoint", "data_table", "ggplot2", "plyr"], "broken": true }, "SJava": { "name": "SJava", "version": "0.96.0", "sha256": "17qvrd8n0vrn9fn9p31s2bhzf6064hnf89c54hbx3flzki73waaz", "depends": [], "broken": true }, "SLGI": { "name": "SLGI", "version": "1.30.0", "sha256": "1pardqmvmi4877q09n3379wq57pyqla53s8gxvygrqny2drb5crj", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "GO_db", "ScISI", "lattice"], "broken": true }, "SMAP": { "name": "SMAP", "version": "1.34.0", "sha256": "07mdnmirsbz8m5zky169q2mqdn1sdh1nlx8qsgdf8h0n0vcs2h3z", "depends": [], "broken": true }, "SNPchip": { "name": "SNPchip", "version": "2.16.0", "sha256": "1fxskvkzn0mfcg2zjs2r2fr0pifrha54a15vbxxcawy4pggf7fdv", "depends": ["Biobase", "GenomeInfoDb", "GenomicRanges", "IRanges", "SummarizedExperiment", "foreach", "lattice", "oligoClasses"], "broken": true }, "SQUADD": { "name": "SQUADD", "version": "1.20.0", "sha256": "1nxf68waqnm9jaj0r8z1499kw5c6l1sykj38wikcc39bsyy23kxm", "depends": ["RColorBrewer"], "broken": true }, "SSPA": { "name": "SSPA", "version": "2.10.0", "sha256": "1835g6chjrl1kz5zc710jy0lx04b84khk2kx981ga6rmlihn5xyc", "depends": ["lattice", "limma", "qvalue"], "broken": true }, "STAN": { "name": "STAN", "version": "1.4.0", "sha256": "0phrznzv3n9nvjbxb172ywxcc6dfjz2gw21w4nzxiwcjaf3kg841", "depends": ["Rsolnp"], "broken": true }, "STROMA4": { "name": "STROMA4", "version": "1.24.0", "sha256": "1x3zgxkcck8ffh89mql45cp54c94n64kf9x6dan9wl24bj3x869f", "depends": ["Biobase", "BiocParallel", "cluster", "matrixStats"], "broken": true }, "STdeconvolve": { "name": "STdeconvolve", "version": "1.8.0", "sha256": "0pyyxmh4bnavsdw6riv72y5m8l53mfr0lpiy9mh0qn57rlmw5fr9", "depends": ["BiocParallel", "Matrix", "clue", "ggplot2", "mgcv", "reshape2", "scatterpie", "slam", "topicmodels", "viridis"], "broken": true }, "SVM2CRM": { "name": "SVM2CRM", "version": "1.2.0", "sha256": "06jhyvq3j35skvkf57iqfphypsv43k12i0wybhhvx4wjsdrrhmwq", "depends": ["AnnotationDbi", "GenomicRanges", "IRanges", "LiblineaR", "ROCR", "SVM2CRMdata", "mclust", "pls", "rtracklayer", "squash", "verification", "zoo"], "broken": true }, "ScISI": { "name": "ScISI", "version": "1.42.0", "sha256": "0bmpl2zaalwxhhc9vj9v3x8ig6hbj4lrbfl2dxmivgsh1hqvbcli", "depends": ["AnnotationDbi", "GO_db", "RpsiXML", "annotate", "apComplex", "org_Sc_sgd_db"], "broken": true }, "SimBindProfiles": { "name": "SimBindProfiles", "version": "1.8.0", "sha256": "1cyqlzb6vykxndslwvmj9sn7hzrq3lqjwsmvkvl7ivfigrslg142", "depends": ["Biobase", "Ringo", "limma", "mclust"], "broken": true }, "SomatiCA": { "name": "SomatiCA", "version": "2.1.0", "sha256": "1a4c8hnl93mnqmm9abc2njcqrlynzbsf39im2gi3ypyjnzabs7m8", "depends": ["DNAcopy", "GenomicRanges", "IRanges", "doParallel", "foreach", "lars", "mvtnorm", "rebmix", "sn"], "broken": true }, "SpacePAC": { "name": "SpacePAC", "version": "1.8.0", "sha256": "11szjavnv8b3sdqdzda3vsx3rbzmnzdimm4b37lm3rfqzrs14qhc", "depends": ["iPAC"], "broken": true }, "SpidermiR": { "name": "SpidermiR", "version": "1.32.0", "sha256": "07s421c8ashww8x99ac18fy1lvjl4zmm3jsz0fggw1gvii172c1x", "depends": ["AnnotationDbi", "gdata", "httr", "igraph", "miRNAtap", "miRNAtap_db", "org_Hs_eg_db"], "broken": true }, "StarBioTrek": { "name": "StarBioTrek", "version": "1.28.0", "sha256": "0cpgn0zcimg18yybfgrjzdczsinvx6n81jjm850gbi76ararq8sc", "depends": ["AnnotationDbi", "e1071", "ggplot2", "graphite", "igraph", "MLmetrics", "reshape2", "ROCR", "SpidermiR"], "broken": true }, "Starr": { "name": "Starr", "version": "1.26.0", "sha256": "0ra9x1kzr0r2wa1ihapzmldq0fdr91rfbbglmzjnq92wrw6rvkd2", "depends": ["MASS", "Ringo", "affxparser", "affy", "pspline", "zlibbioc"], "broken": true }, "SummarizedBenchmark": { "name": "SummarizedBenchmark", "version": "2.20.0", "sha256": "16gzlkyf76fcd46ck417sxh86smivmaggqvyg0v9v0f4jac7610g", "depends": ["BiocGenerics", "BiocParallel", "crayon", "digest", "dplyr", "ggplot2", "mclust", "rlang", "S4Vectors", "sessioninfo", "stringr", "SummarizedExperiment", "tibble", "tidyr", "UpSetR"], "broken": true }, "Sushi": { "name": "Sushi", "version": "1.8.0", "sha256": "1ldvv1028chnh8ng85534k924cgdmzqb3i18z6xpacsjgg5k7s7l", "depends": ["biomaRt", "zoo"], "broken": true }, "SwimR": { "name": "SwimR", "version": "1.8.0", "sha256": "0vwjrpm4qbhc8afv0zj0al3rv06izp649kz8h3pb1yixw4bwrxg8", "depends": ["R2HTML", "gplots", "signal"], "broken": true }, "TCGAbiolinksGUI": { "name": "TCGAbiolinksGUI", "version": "1.23.0", "sha256": "16757szccczlv1q35y1cnmlkr12s46f63z7ijffpb15q85xlaqdx", "depends": ["caret", "clusterProfiler", "colourpicker", "data_table", "downloader", "DT", "ELMER", "ggplot2", "ggrepel", "maftools", "pathview", "plotly", "readr", "sesame", "shiny", "shinyBS", "shinydashboard", "shinyFiles", "shinyjs", "stringr", "SummarizedExperiment", "TCGAbiolinks", "TCGAbiolinksGUI_data"], "broken": true }, "TDARACNE": { "name": "TDARACNE", "version": "1.20.0", "sha256": "0jf89s2bnz8psd7vqh3l29ch5mb2ilky2jmv8db4kcqaw9157kn8", "depends": ["Biobase", "Rgraphviz"], "broken": true }, "TNBC_CMS": { "name": "TNBC.CMS", "version": "1.18.0", "sha256": "1syygq9br5icbjbmi1kq9gs7g3bw1vzmy8mlf8ga2rk1lw6ika90", "depends": ["e1071", "forestplot", "GGally", "ggplot2", "ggpubr", "GSVA", "pheatmap", "pracma", "quadprog", "R_utils", "RColorBrewer", "SummarizedExperiment", "survival"], "broken": true }, "TSRchitect": { "name": "TSRchitect", "version": "1.20.0", "sha256": "1v9zz8ny9rwkyz98cv49l9ilh68h8mvm2x44n8i8rvjayc50zi9i", "depends": ["AnnotationHub", "BiocGenerics", "BiocParallel", "dplyr", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "gtools", "IRanges", "readxl", "Rsamtools", "rtracklayer", "S4Vectors", "SummarizedExperiment"], "broken": true }, "TSSi": { "name": "TSSi", "version": "1.16.2", "sha256": "0lvvzhm0npm9hc7n9rw9ipqgp7kgyvciapai0y8l4r3c07wh8nbs", "depends": ["Biobase", "BiocGenerics", "Hmisc", "IRanges", "S4Vectors", "minqa", "plyr"], "broken": true }, "TarSeqQC": { "name": "TarSeqQC", "version": "1.0.3", "sha256": "06a9kvyx73ysllid9mafgyp1czhyf06gxma1b6bkyksingpgnb68", "depends": ["BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "cowplot", "ggplot2", "openxlsx", "plyr", "reshape2"], "broken": true }, "TimeSeriesExperiment": { "name": "TimeSeriesExperiment", "version": "1.13.0", "sha256": "0bdpxxr739qdg92qabfx122k9f43vw2hyxp4yxqlbp37vzgcdf2c", "depends": ["DESeq2", "dplyr", "dynamicTreeCut", "edgeR", "ggplot2", "Hmisc", "limma", "magrittr", "proxy", "S4Vectors", "SummarizedExperiment", "tibble", "tidyr", "vegan", "viridis"], "broken": true }, "TimiRGeN": { "name": "TimiRGeN", "version": "1.11.0", "sha256": "104j3rdl1mfklqvpsr753zlplr001cqbkphbhf2xrcfw8si7bgr2", "depends": ["biomaRt", "clusterProfiler", "dplyr", "FreqProf", "ggdendro", "gghighlight", "ggplot2", "gplots", "gtools", "igraph", "Mfuzz", "MultiAssayExperiment", "RCy3", "readxl", "reshape2", "rWikiPathways", "scales", "stringr", "tidyr"], "broken": true }, "ToPASeq": { "name": "ToPASeq", "version": "1.4.0", "sha256": "18fwifmih7x4wr7s3nr8qwvxbp0a33qj39sfwkvhr97jqdggb78j", "depends": ["AnnotationDbi", "Biobase", "DESeq", "DESeq2", "GenomicRanges", "KEGGgraph", "RBGL", "R_utils", "Rcpp", "Rgraphviz", "TeachingDemos", "clipper", "doParallel", "edgeR", "fields", "gRbase", "graph", "graphite", "limma", "locfit", "qpgraph"], "broken": true }, "TraRe": { "name": "TraRe", "version": "1.5.0", "sha256": "06w5rk2wjam5dhiya9n6kjbjahw4i46cb05zvakcy0f8gwrvb9ic", "depends": ["BiocParallel", "dqrng", "ggplot2", "glmnet", "gplots", "gtools", "hash", "igraph", "matrixStats", "pvclust", "R_utils", "SummarizedExperiment"], "broken": true }, "TransView": { "name": "TransView", "version": "1.14.0", "sha256": "02as66pzhgls2papji5mqpaczvdfpi6af0mafip8i9hj06z41wci", "depends": ["GenomicRanges", "IRanges", "Rsamtools", "gplots", "zlibbioc"], "broken": true }, "Travel": { "name": "Travel", "version": "1.6.0", "sha256": "074v9hl4gzy8081mlas3mjaplchjrmk2bl4f5nkdjclh46xf3wgg", "depends": ["Rcpp"], "broken": true }, "TypeInfo": { "name": "TypeInfo", "version": "1.36.0", "sha256": "0f0cllsf0pw2bgvq9fhfksqsxb2820js5y125vhcr0ns5kcvi07y", "depends": [], "broken": true }, "Vega": { "name": "Vega", "version": "1.18.0", "sha256": "0f7rzzckd69xbnism0v7jl0dly55lwj30nla7yj88qqalnb7ajzs", "depends": [], "broken": true }, "XBSeq": { "name": "XBSeq", "version": "1.0.2", "sha256": "01h3hj4mm7dr16vwbra5iazrgar9nbh2gs2gklyx0wqjfzm3gj49", "depends": ["Biobase", "DESeq2", "Delaporte", "dplyr", "ggplot2", "locfit", "magrittr", "matrixStats", "pracma"], "broken": true }, "XCIR": { "name": "XCIR", "version": "1.7.0", "sha256": "0n42pw01wv1sk06hby9kwijx6zwaw4lrlpsa0wlkrkf323slkllw", "depends": ["biomaRt", "data_table", "ggplot2", "IRanges", "readxl", "S4Vectors", "seqminer", "VariantAnnotation"], "broken": true }, "affyPara": { "name": "affyPara", "version": "1.30.0", "sha256": "14g7xrzsqqsr2h20nv000dd3v71wq18bq78r345w29fs53kipxxd", "depends": ["affy", "affyio", "aplpack", "snow", "vsn"], "broken": true }, "affyQCReport": { "name": "affyQCReport", "version": "1.48.0", "sha256": "0cw6z8idar5qa9y3svrm5fdimdamb2xjjj59d107h2in7bvgni7j", "depends": ["Biobase", "RColorBrewer", "affy", "affyPLM", "genefilter", "lattice", "simpleaffy", "xtable"], "broken": true }, "affypdnn": { "name": "affypdnn", "version": "1.44.0", "sha256": "1av7a8w86wcslbl3q2zbnga8rww3n7dmwdywq4fm86pbmwh1jz9v", "depends": ["affy"], "broken": true }, "alpine": { "name": "alpine", "version": "1.26.0", "sha256": "1md4m9ln1mpxf7d2h7jnsjyi4zrviiqn9fzk1gkz2n6qj7jwpqbb", "depends": ["Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "graph", "IRanges", "RBGL", "Rsamtools", "S4Vectors", "speedglm", "stringr", "SummarizedExperiment"], "broken": true }, "alsace": { "name": "alsace", "version": "1.6.0", "sha256": "1vrwi2rkccgiwgshz5rxyr55dl7awbh1drbhhsrbpjsbzxwmiv4a", "depends": ["ALS", "ptw"], "broken": true }, "ampliQueso": { "name": "ampliQueso", "version": "1.8.0", "sha256": "0v21y2nd0qwnag0n6h0krr9c0vpv6ig89d0jsi58x3pi5m0mypip", "depends": ["DESeq", "VariantAnnotation", "doParallel", "edgeR", "foreach", "genefilter", "ggplot2", "gplots", "knitr", "rgl", "rnaSeqMap", "samr", "statmod", "xtable"], "broken": true }, "beadarraySNP": { "name": "beadarraySNP", "version": "1.36.0", "sha256": "1dj5zi9lkyq5lgrcmr08cjdv3ysfa6p9zc8jza8mm6vy14qsl5ah", "depends": ["Biobase", "quantsmooth"], "broken": true }, "betr": { "name": "betr", "version": "1.26.0", "sha256": "1rs2xajrac3a4sk88i7zq3v849969iw0k8wmpbc0ihw9m4ljb0sx", "depends": ["Biobase", "limma", "mvtnorm"], "broken": true }, "bgafun": { "name": "bgafun", "version": "1.32.0", "sha256": "1wakjjdcgzl9snsa9i1f7kk0ppwiccxmznd93yawvjk74gqwnkp3", "depends": ["ade4", "made4", "seqinr"], "broken": true }, "bgx": { "name": "bgx", "version": "1.36.0", "sha256": "1x0i4llp6yrfybp7lwqwc7kb1s12dl8a0nwymhjd3fkfv5lslfbx", "depends": ["Biobase", "affy", "gcrma"], "broken": true }, "bigPint": { "name": "bigPint", "version": "1.15.0", "sha256": "1r9gr5f9as09ifagal5k7713h95qjw508cf8ny3j1jmqd24v6xhs", "depends": ["DelayedArray", "dplyr", "GGally", "ggplot2", "gridExtra", "hexbin", "Hmisc", "htmlwidgets", "plotly", "plyr", "RColorBrewer", "reshape", "shiny", "shinycssloaders", "shinydashboard", "stringr", "SummarizedExperiment", "tidyr"], "broken": true }, "bigmemoryExtras": { "name": "bigmemoryExtras", "version": "1.14.2", "sha256": "05ksk3phvh4wc3vgfj5bl1jfxhndia90bkq9s91wfjzcfkrd41q8", "depends": ["Biobase", "bigmemory"], "broken": true }, "biodbExpasy": { "name": "biodbExpasy", "version": "1.8.1", "sha256": "0n5avxhv5131122h18d3r2v9c64i3nb251hmz8hhc6chmk203fmj", "depends": ["R6", "biodb", "chk", "stringr"], "broken": true }, "biodbKegg": { "name": "biodbKegg", "version": "1.10.2", "sha256": "0rwxbg3ij5rg3agzsxib7f80b05ar40xnql2krl44c3n43yqkwyw", "depends": ["R6", "biodb", "chk", "lifecycle"], "broken": true }, "biodbLipidmaps": { "name": "biodbLipidmaps", "version": "1.10.0", "sha256": "1p181kwy9q8jj4m7flg71pqn7h6865hbwha4n6j2qki830vym6rv", "depends": ["R6", "biodb", "lifecycle"], "broken": true }, "biodbMirbase": { "name": "biodbMirbase", "version": "1.5.0", "sha256": "17clip9l8as9pz390bqgj07jxp1rijis2f5hj53s6vqaqmiyz4il", "depends": ["biodb", "chk", "R6", "stringr"], "broken": true }, "biosvd": { "name": "biosvd", "version": "2.6.0", "sha256": "0mjkan7drib9v49dk3rnrkydm1dxfqimk5gk4jm9qv8kdfcjk0zh", "depends": ["Biobase", "BiocGenerics", "NMF"], "broken": true }, "birta": { "name": "birta", "version": "1.14.0", "sha256": "1pszpvmvjp1r0bwj7w9ws0y8xmb3yfmq5gifj9jwvgw2p7y718zr", "depends": ["Biobase", "MASS", "limma"], "broken": true }, "birte": { "name": "birte", "version": "1.6.1", "sha256": "08jkjlkjswz3x4sxw80xr9ck6277ag1gzv5y1dxh7aa6i644w48p", "depends": ["Biobase", "MASS", "Rcpp", "RcppArmadillo", "glmnet", "limma", "nem"], "broken": true }, "brainflowprobes": { "name": "brainflowprobes", "version": "1.16.0", "sha256": "06gga72ns7h9c6mdbvbj8afpkyizg7maazriilvaq433h6s1pgqb", "depends": ["Biostrings", "BSgenome_Hsapiens_UCSC_hg19", "bumphunter", "cowplot", "derfinder", "derfinderPlot", "GenomicRanges", "GenomicState", "ggplot2", "RColorBrewer"], "broken": true }, "bridge": { "name": "bridge", "version": "1.34.0", "sha256": "08lfbczaj7hkgqfsm060z56anx1yvsfwknzw40gq919k0zm9vfcf", "depends": ["rama"], "broken": true }, "caOmicsV": { "name": "caOmicsV", "version": "1.0.0", "sha256": "0162h17szpr98g4lgz5nypcrslk4103hdn5qdxfxv6frssn9l9g3", "depends": ["bc3net", "igraph"], "broken": true }, "cellGrowth": { "name": "cellGrowth", "version": "1.14.0", "sha256": "0d40kll2rkzijyk0d0xb9rzyck5r0hkybv0j1ba72g9kk2mdmz7z", "depends": ["lattice", "locfit"], "broken": true }, "cellHTS": { "name": "cellHTS", "version": "1.40.2", "sha256": "1cdzrmqr3fwxylc3m7g72bmc5iml266355i0mfdavp2q9y28kc85", "depends": ["Biobase", "RColorBrewer", "genefilter", "prada"], "broken": true }, "cellHTS2": { "name": "cellHTS2", "version": "2.34.1", "sha256": "068lqpxhy04fhpma8cbd79jwg0cifvg8qhav5a4p22dgmalvajw1", "depends": ["Biobase", "Category", "GSEABase", "RColorBrewer", "genefilter", "hwriter", "locfit", "prada", "splots", "vsn"], "broken": true }, "cellTree": { "name": "cellTree", "version": "1.27.0", "sha256": "0yfr59fcbdj03ikkpvw1qcxqrjbkz7nkfmb5m1xr4k9qs39bq9sb", "depends": ["gplots", "igraph", "maptpx", "slam", "topGO", "topicmodels", "xtable"], "broken": true }, "charm": { "name": "charm", "version": "2.16.1", "sha256": "00bvgpj705v9jb43skj5iljjf131dnz90n2rc1yww6s2kh4qqppm", "depends": ["BSgenome", "Biobase", "Biostrings", "IRanges", "RColorBrewer", "SQN", "ff", "fields", "genefilter", "gtools", "limma", "nor1mix", "oligo", "oligoClasses", "preprocessCore", "siggenes", "sva"], "broken": true }, "chimera": { "name": "chimera", "version": "1.12.0", "sha256": "11arbg6c76rx4zyylp6ga8ygx8890h0pkg4ciwhy4xc8x1smmq7r", "depends": ["AnnotationDbi", "BSgenome_Hsapiens_UCSC_hg19", "Biobase", "GenomicAlignments", "GenomicRanges", "Homo_sapiens", "Rsamtools", "TxDb_Hsapiens_UCSC_hg19_knownGene"], "broken": true }, "chroGPS": { "name": "chroGPS", "version": "1.14.0", "sha256": "0i0hrf38sjsay6r6zh69cy6xki17cjw427szq4h7770jlphiq8n1", "depends": ["Biobase", "ICSNP", "IRanges", "MASS", "changepoint", "cluster"], "broken": true }, "chromstaR": { "name": "chromstaR", "version": "1.32.0", "sha256": "071aipwk1awr71hvzflps49dzp83p12zm1pbyx4l8d2v3wbj0dlz", "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "bamsignals", "chromstaRData", "doParallel", "foreach", "ggplot2", "mvtnorm", "reshape2"], "broken": true }, "chromswitch": { "name": "chromswitch", "version": "1.22.0", "sha256": "007wa8980hkpja33ph3b3fjsjrf91cnwc0a7y4014k8xxmmgfdh7", "depends": ["Biobase", "BiocParallel", "cluster", "dplyr", "GenomicRanges", "gplots", "IRanges", "lazyeval", "magrittr", "matrixStats", "NMF", "rtracklayer", "S4Vectors", "tidyr"], "broken": true }, "clonotypeR": { "name": "clonotypeR", "version": "1.8.0", "sha256": "1fj00hrxijkn002ixa7kn07jq94mlsgz99xr3sapzg0jqacgp9q0", "depends": [], "broken": true }, "coMET": { "name": "coMET", "version": "1.2.1", "sha256": "017sjx9wamyg6jglnbw1ynkbnp9idj9142jhkqvy8xji6kqh5xpk", "depends": ["GenomicRanges", "Gviz", "IRanges", "S4Vectors", "biomaRt", "corrplot", "ggbio", "ggplot2", "gridExtra", "hash", "psych", "rtracklayer", "trackViewer"], "broken": true }, "coRNAi": { "name": "coRNAi", "version": "1.20.0", "sha256": "05jv85jbb5lz0x0cmg52sn6gnsscyq939yyk6ll9061bx51as7cv", "depends": ["MASS", "cellHTS2", "gplots", "lattice", "limma", "locfit"], "broken": true }, "cobindR": { "name": "cobindR", "version": "1.8.0", "sha256": "06nckxm5hz6c336p5fvfmccfzdri68qcmagkyjg7nnfsyl66fri1", "depends": ["BSgenome", "BiocGenerics", "Biostrings", "IRanges", "biomaRt", "gmp", "gplots", "mclust", "seqinr", "yaml"], "broken": true }, "coexnet": { "name": "coexnet", "version": "1.19.1", "sha256": "0zw8a8pqmajqnv5n6i7fn7krwax81sd4c6wqm4zr61fy2blqzv3h", "depends": ["acde", "affy", "Biobase", "GEOquery", "igraph", "limma", "minet", "rmarkdown", "siggenes", "STRINGdb", "SummarizedExperiment", "vsn"], "broken": true }, "compartmap": { "name": "compartmap", "version": "1.18.0", "sha256": "0lvgwnp5cgn96m9y4snpczfbfs72lxbaa36lnmwa7j07jy4s9108", "depends": ["BiocSingular", "DelayedArray", "DelayedMatrixStats", "GenomicRanges", "ggplot2", "HDF5Array", "Matrix", "RaggedExperiment", "reshape2", "RMTstat", "rtracklayer", "scales", "SummarizedExperiment"], "broken": true }, "conclus": { "name": "conclus", "version": "1.5.0", "sha256": "09rk73sxqxsy0zq07n67jxqbzb1rlxlj0phg6987szdjwxmag6jc", "depends": ["AnnotationDbi", "Biobase", "BiocFileCache", "biomaRt", "clusterProfiler", "dbscan", "doParallel", "dplyr", "factoextra", "foreach", "fpc", "GEOquery", "ggplot2", "gridExtra", "org_Hs_eg_db", "org_Mm_eg_db", "pheatmap", "rlang", "Rtsne", "scales", "scater", "scran", "SingleCellExperiment", "stringr", "SummarizedExperiment"], "broken": true }, "contiBAIT": { "name": "contiBAIT", "version": "1.30.0", "sha256": "1asyfx0mbg0pli2g533xmlppfw0s0f1y4vf2rfrnai4chsh1rh0k", "depends": ["BH", "BiocGenerics", "BiocParallel", "clue", "cluster", "colorspace", "data_table", "diagram", "DNAcopy", "exomeCopy", "GenomicAlignments", "GenomicFiles", "GenomicRanges", "ggplot2", "gplots", "gtools", "IRanges", "Rcpp", "reshape2", "Rsamtools", "rtracklayer", "S4Vectors", "TSP"], "broken": true }, "copynumber": { "name": "copynumber", "version": "1.10.0", "sha256": "1g03cy5inbhzhl5hj8vma34xm8lixilhalavjysp93bwg4dfskv6", "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors"], "broken": true }, "crisprseekplus": { "name": "crisprseekplus", "version": "1.26.0", "sha256": "1ccz944jwlcnflrdh1aamfc5b03n6pys65b13f049f0x214vqg68", "depends": ["AnnotationDbi", "BiocManager", "BSgenome", "CRISPRseek", "DT", "GenomicFeatures", "GenomicRanges", "GUIDEseq", "hash", "shiny", "shinyjs"], "broken": true }, "crossmeta": { "name": "crossmeta", "version": "1.30.0", "sha256": "1ghgfby1rl3phldyipli550f0i289yanb0v4nzn5l1xnpkxaj6fa", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocManager", "DBI", "DT", "GEOquery", "RCurl", "RSQLite", "XML", "affxparser", "affy", "data_table", "edgeR", "fdrtool", "limma", "matrixStats", "metaMA", "miniUI", "oligo", "reader", "readxl", "shiny", "shinyBS", "shinyWidgets", "shinyjs", "shinypanel", "stringr", "sva", "tibble"], "broken": true }, "ctgGEM": { "name": "ctgGEM", "version": "1.7.0", "sha256": "0hmapz96r024r3bws1wf0spd0i81viyma859y9nn93jrwxscrcdb", "depends": ["Biobase", "BiocGenerics", "igraph", "Matrix", "monocle", "sincell", "SummarizedExperiment", "TSCAN"], "broken": true }, "cytofkit": { "name": "cytofkit", "version": "1.2.4", "sha256": "1pgaw18m4z3az3b0d5d2wlvfq0ha80k5bc0vyjd9grlbwcpvs6nr", "depends": ["Biobase", "RANN", "Rcpp", "Rtsne", "VGAM", "doParallel", "e1071", "flowCore", "ggplot2", "gplots", "igraph", "pdist", "plyr", "reshape", "reshape2", "shiny", "vegan"], "broken": true }, "dasper": { "name": "dasper", "version": "1.9.0", "sha256": "095ldl40cay5n8lkp8y69lbmflhnbwm1b075s4zgpagn81awp0cn", "depends": ["basilisk", "BiocFileCache", "BiocParallel", "data_table", "dplyr", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "ggplot2", "ggpubr", "ggrepel", "IRanges", "magrittr", "megadepth", "plyranges", "readr", "reticulate", "rtracklayer", "S4Vectors", "stringr", "SummarizedExperiment", "tidyr"], "broken": true }, "ddgraph": { "name": "ddgraph", "version": "1.14.0", "sha256": "0nmrz9cy7l31vym3fcc9m3dmgmbnd5r91p3fxpziaarphi27zszl", "depends": ["MASS", "RColorBrewer", "Rcpp", "bnlearn", "graph", "gtools", "pcalg", "plotrix"], "broken": true }, "deco": { "name": "deco", "version": "1.13.0", "sha256": "0d4abif3v62cbas6hl7pfw8q8jihh7nsra76k9cm6kz54qw4fbnw", "depends": ["ade4", "AnnotationDbi", "Biobase", "BiocParallel", "BiocStyle", "cluster", "foreign", "gdata", "ggplot2", "gplots", "gridExtra", "limma", "locfit", "made4", "RColorBrewer", "reshape2", "scatterplot3d", "sfsmisc", "SummarizedExperiment"], "broken": true }, "dexus": { "name": "dexus", "version": "1.10.0", "sha256": "0hc28mkmnr37fmw6xw2cywla946gm0cxa8k4hi32d12cm9c24xqx", "depends": ["BiocGenerics"], "broken": true }, "diffloop": { "name": "diffloop", "version": "1.24.0", "sha256": "0v0jg9y08xzw775x2lm82ig1ag4wjf4z2l6a66zmk6qbn59dwj1g", "depends": ["Biobase", "biomaRt", "data_table", "dplyr", "edgeR", "foreach", "GenomeInfoDb", "GenomicRanges", "ggplot2", "IRanges", "limma", "locfit", "matrixStats", "pbapply", "plyr", "readr", "reshape2", "rtracklayer", "S4Vectors", "statmod", "Sushi"], "broken": true }, "domainsignatures": { "name": "domainsignatures", "version": "1.30.0", "sha256": "0rr5d57cjkp46qp2908vh3wyfdgiyaikdgbcxipizcv5a00nq0rx", "depends": ["AnnotationDbi", "KEGG_db", "biomaRt", "prada"], "broken": true }, "dpeak": { "name": "dpeak", "version": "1.12.0", "sha256": "1fx2rrcqmjckk5kk3mfa56b1393b2c8sf566q95d8zmlsvkl03w5", "depends": ["BSgenome", "IRanges", "MASS", "Rcpp"], "broken": true }, "dualKS": { "name": "dualKS", "version": "1.30.0", "sha256": "02j9l73brxa4fgsp9cbd3w7dxllvj744rby21dkfnw2c42rcxpvz", "depends": ["Biobase", "affy"], "broken": true }, "eegc": { "name": "eegc", "version": "1.26.0", "sha256": "0m67zjsq2xzk292rp0hdlj8lbfgci2dsdb5hmn4b591fqawwsqbb", "depends": ["AnnotationDbi", "clusterProfiler", "DESeq2", "DOSE", "edgeR", "ggplot2", "gplots", "igraph", "limma", "org_Hs_eg_db", "org_Mm_eg_db", "pheatmap", "R_utils", "S4Vectors", "sna", "wordcloud"], "broken": true }, "eisa": { "name": "eisa", "version": "1.22.0", "sha256": "0p3s6z7s4d165h4w5g1h273626h5j255c0hyjv5dlrdhr4ign7v6", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "Category", "DBI", "genefilter", "isa2"], "broken": true }, "enrichTF": { "name": "enrichTF", "version": "1.18.0", "sha256": "0lhmlxw7mpb76w2agm25v5qzxgf28wfw2xc0fnlqn2sbbfj295y9", "depends": ["BiocGenerics", "BSgenome", "clusterProfiler", "GenomeInfoDb", "GenomicRanges", "ggplot2", "ggpubr", "heatmap3", "IRanges", "JASPAR2018", "magrittr", "motifmatchr", "pipeFrame", "R_utils", "rmarkdown", "rtracklayer", "S4Vectors", "TFBSTools"], "broken": true }, "ensemblVEP": { "name": "ensemblVEP", "version": "1.10.3", "sha256": "1q9bzs9zqk2xv10jnq7571f8wgyi2l6zk6sgd4sja6fw82lrnmsy", "depends": ["BiocGenerics", "Biostrings", "GenomicRanges", "VariantAnnotation"], "broken": true }, "epihet": { "name": "epihet", "version": "1.13.0", "sha256": "1p5sgb438yj6h0fv0v17dhz1pl32vai5zcbmgpgagrd5829a6a7r", "depends": ["data_table", "doParallel", "foreach", "GenomicRanges", "ggplot2", "igraph", "IRanges", "pheatmap", "qvalue", "ReactomePA", "Rtsne", "S4Vectors", "WGCNA"], "broken": true }, "exomeCopy": { "name": "exomeCopy", "version": "1.16.0", "sha256": "09awyyfgs0k639nqrcrbq1k875qlyac1146w4ay6nxgijqy7iv82", "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools"], "broken": true }, "exomePeak": { "name": "exomePeak", "version": "2.2.2", "sha256": "03xj0h1cgxzbp2fk830l771jmmcll1bq81xips8hjgng3ywz5m1a", "depends": ["GenomicAlignments", "GenomicFeatures", "Rsamtools", "rtracklayer"], "broken": true }, "exomePeak2": { "name": "exomePeak2", "version": "1.14.3", "sha256": "1hvz18hlvljbv0cmdlxzvsl2ysb5m0c5qq2y8jxzsby3zxlqplph", "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "BSgenome", "DESeq2", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "IRanges", "magrittr", "mclust", "Rsamtools", "rtracklayer", "S4Vectors", "speedglm", "SummarizedExperiment"], "broken": true }, "explorase": { "name": "explorase", "version": "1.34.0", "sha256": "108p864qq8zh4x7p765ygrdkj4r0vm3s2fmi3scswkhcv3vjcjg3", "depends": ["limma"], "broken": true }, "facopy": { "name": "facopy", "version": "1.4.1", "sha256": "07ggz86c48rz8asqvfglrvsimnzh3ii43kzpm8ji6sd43i141650", "depends": ["DOSE", "FactoMineR", "GO_db", "GOstats", "IRanges", "MASS", "Rgraphviz", "annotate", "coin", "data_table", "facopy_annot", "ggplot2", "graphite", "gridExtra", "igraph", "nnet", "reshape2", "scales"], "broken": true }, "farms": { "name": "farms", "version": "1.22.0", "sha256": "1jmx5rajm6fkhx5gfpwh8nsqw0plhfzy1bibvkdf83arxjjr6s59", "depends": ["Biobase", "MASS", "affy"], "broken": true }, "fcoex": { "name": "fcoex", "version": "1.13.0", "sha256": "085r5s5sqrj2701zk5kv3818ksxvxzd76lknzi6bk1svw4d3lsyc", "depends": ["clusterProfiler", "data_table", "dplyr", "FCBF", "ggplot2", "ggrepel", "igraph", "intergraph", "Matrix", "network", "pathwayPCA", "progress", "scales", "SingleCellExperiment", "sna", "stringr"], "broken": true }, "flipflop": { "name": "flipflop", "version": "1.8.2", "sha256": "1v4ihrmw0vphz0k0f37qy5k8zwa5g5cnj4agccjl4mqbvwiq4awh", "depends": ["GenomicRanges", "IRanges", "Matrix"], "broken": true }, "flowCL": { "name": "flowCL", "version": "1.8.0", "sha256": "064946w944gw7l0hizw974i21cahzvfj1xza8f7ay9rx2baz28sh", "depends": ["Rgraphviz"], "broken": true }, "flowFit": { "name": "flowFit", "version": "1.8.0", "sha256": "1fja1d5irh71a3rqdsbw5sb14ss2xmird6vxcps96r6s6rz2bra3", "depends": ["flowCore", "flowViz", "gplots", "kza", "minpack_lm"], "broken": true }, "flowMap": { "name": "flowMap", "version": "1.8.0", "sha256": "0rkdspl9lnasc8axlsx076g14pkgwrlz9nbxy0f1z67w991d823p", "depends": ["Matrix", "abind", "ade4", "doParallel", "reshape2", "scales"], "broken": true }, "flowQ": { "name": "flowQ", "version": "1.30.0", "sha256": "1yz0w0bpv98l319y8dw82qaykg6w70sxpzmhxdckwdqjpixq5sf5", "depends": ["BiocGenerics", "IRanges", "RColorBrewer", "bioDist", "flowCore", "flowViz", "geneplotter", "lattice", "latticeExtra", "mvoutlier", "outliers", "parody"], "broken": true }, "flowQB": { "name": "flowQB", "version": "1.14.0", "sha256": "1swsdqra8w8z27p2mv1q37ydak7rjifxm78h5x6mhv1vfq4faz12", "depends": ["Biobase", "MASS", "flowCore"], "broken": true }, "flowType": { "name": "flowType", "version": "2.8.2", "sha256": "0q7bk8pn71zyzc1m16rqimlyldnfj178k64vg0kw4yiwdjxlgdr4", "depends": ["BH", "Biobase", "Rcpp", "flowClust", "flowCore", "flowMeans", "flowMerge", "rrcov", "sfsmisc"], "broken": true }, "flowUtils": { "name": "flowUtils", "version": "1.34.0", "sha256": "0qba66cfsy8facvdpnl5jf71xwaqs3w6j2z0ph7c39zyng0nibwp", "depends": ["Biobase", "RUnit", "XML", "corpcor", "flowCore", "flowViz", "graph"], "broken": true }, "focalCall": { "name": "focalCall", "version": "1.4.0", "sha256": "1dqk0lda24lkhfsid15c6n121s63zbk6658za5qxqkxdd82z7axf", "depends": ["CGHcall"], "broken": true }, "gCMAP": { "name": "gCMAP", "version": "1.14.0", "sha256": "09dcaq0763kb399wh232n6r1s8qkj0c4zcmpjp6cz08w6n7lchgx", "depends": ["AnnotationDbi", "Biobase", "Category", "DESeq", "GSEABase", "GSEAlm", "Matrix", "annotate", "genefilter", "limma"], "broken": true }, "gCMAPWeb": { "name": "gCMAPWeb", "version": "1.10.0", "sha256": "00qx90gycqqca8b3brkl0bkckn7saqz9z38vinhjxlyaanc9v6ml", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "GSEABase", "Rook", "annotate", "brew", "gCMAP", "hwriter", "yaml"], "broken": true }, "gQTLBase": { "name": "gQTLBase", "version": "1.2.1", "sha256": "1a1ndjjp2zn1lsfahpvi3xhkdgwl5wk0bdm7kc92aidq50a2db42", "depends": ["BBmisc", "BatchJobs", "BiocGenerics", "GenomicFiles", "GenomicRanges", "S4Vectors", "bit", "doParallel", "ff", "foreach", "rtracklayer"], "broken": true }, "gQTLstats": { "name": "gQTLstats", "version": "1.2.0", "sha256": "1cwri36z85zyyr48dkkl7qkgbx9fpv7y38mbbm470adc7ac56zbv", "depends": ["AnnotationDbi", "BatchJobs", "Biobase", "BiocGenerics", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "doParallel", "dplyr", "foreach", "gQTLBase", "gam", "ggplot2", "limma", "reshape2", "snpStats"], "broken": true }, "gaggle": { "name": "gaggle", "version": "1.38.0", "sha256": "0bl60nca27rkij061h6g16ddlkq29rb1wh5pr2hz87y74pmb8m2w", "depends": ["RUnit", "graph", "rJava"], "broken": true }, "gaia": { "name": "gaia", "version": "2.14.0", "sha256": "099imzsa7pghp7qbxjjnfrqc8zkn25wm5xj9jn40m9as11zxdrsx", "depends": [], "broken": true }, "gaucho": { "name": "gaucho", "version": "1.6.0", "sha256": "1c1aaidhdv9rr2v3q6832q0ajc3g7l4gfx1rhf27kv4pn1j5s23s", "depends": ["GA", "Rgraphviz", "graph", "png"], "broken": true }, "geecc": { "name": "geecc", "version": "1.4.0", "sha256": "00dkp4ldnpadvw6fdva0gg0m843j7i667r0i33c9dsrjfc7k7z8q", "depends": ["MASS", "gplots"], "broken": true }, "genbankr": { "name": "genbankr", "version": "1.27.0", "sha256": "0fv87cf2y10ijlb0g1x9g9wh95qyljqb1c7k1ihbnjcg36xkh8lc", "depends": ["Biobase", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "rtracklayer", "S4Vectors", "VariantAnnotation"], "broken": true }, "genoset": { "name": "genoset", "version": "1.24.0", "sha256": "0xxh23sdb5qjfh97a2psp70zb54zx40x8501bpp7gzgqbfn1wf7w", "depends": ["Biobase", "BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment"], "broken": true }, "genotypeeval": { "name": "genotypeeval", "version": "1.0.0", "sha256": "1clljhqy57yy0ss9700zfnsgnby3dism8z2682xjhzzprg049cx4", "depends": ["BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicRanges", "IRanges", "VariantAnnotation", "ggplot2", "rtracklayer"], "broken": true }, "genphen": { "name": "genphen", "version": "1.24.0", "sha256": "1m60qagcxviix4zjzfhvrwchbjq2clss6mivb8q07bcq369yw1b8", "depends": ["Biostrings", "doParallel", "e1071", "foreach", "ranger", "Rcpp", "rPref", "rstan"], "broken": true }, "gespeR": { "name": "gespeR", "version": "1.2.0", "sha256": "0s8lndwwqkkkiyqzi8xpqz6clzjrkmkkrh2f1ch80hvfj83rb89d", "depends": ["Biobase", "Matrix", "biomaRt", "cellHTS2", "doParallel", "dplyr", "foreach", "ggplot2", "glmnet", "reshape2"], "broken": true }, "gpart": { "name": "gpart", "version": "1.13.0", "sha256": "1518wjkaw22ckgpwl6si83bhijvib0r0kgs9s4das41f0ygi92sd", "depends": ["AnnotationDbi", "biomaRt", "data_table", "GenomicRanges", "Homo_sapiens", "igraph", "IRanges", "OrganismDbi", "Rcpp", "TxDb_Hsapiens_UCSC_hg38_knownGene"], "broken": true }, "gprege": { "name": "gprege", "version": "1.14.0", "sha256": "0mc8x8faj8pf8zb3mywjscn2rzs7bc0ws507a32r7zl5j8p9rzag", "depends": [], "broken": true }, "htSeqTools": { "name": "htSeqTools", "version": "1.16.0", "sha256": "1bjbagx6s66fiia71n7ljg5rfc2v22bbp2sk718mf1i9i38c58lm", "depends": ["BSgenome", "Biobase", "BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "MASS"], "broken": true }, "iPAC": { "name": "iPAC", "version": "1.14.0", "sha256": "1gzxv6jkn7crylklmnvhm86gczmsr80dmw1a7flaisiiy40k128g", "depends": ["Biostrings", "gdata", "multtest", "scatterplot3d"], "broken": true }, "imageHTS": { "name": "imageHTS", "version": "1.20.0", "sha256": "1dg8cmrnzlv2qm5lf9771fiir5l0cql6pmfmv0l3037wisdgz1jw", "depends": ["Biobase", "EBImage", "cellHTS2", "e1071", "hwriter", "vsn"], "broken": true }, "inSilicoDb": { "name": "inSilicoDb", "version": "2.6.0", "sha256": "1avxm8qm9rblck94v0aq0na70jfl2cyr9xmbbk27n5hgp1cnaizf", "depends": ["Biobase", "RCurl", "rjson"], "broken": true }, "inSilicoMerging": { "name": "inSilicoMerging", "version": "1.14.0", "sha256": "1xiq66b0vjrcxf4nbmk5mmn1dlxbpa879z04f00w3yz1k7rx6782", "depends": ["Biobase"], "broken": true }, "inveRsion": { "name": "inveRsion", "version": "1.18.0", "sha256": "05jwxwjyvkilfmygf16k3d55ma7s1ya7lyxh8v4pd8gql7v3kllq", "depends": ["haplo_stats"], "broken": true }, "iontree": { "name": "iontree", "version": "1.16.0", "sha256": "1pamgkg85qi3iqqws7a3l8lph428alz1dzf08x309njqz8cbzw91", "depends": ["RSQLite", "XML", "rJava"], "broken": true }, "iterClust": { "name": "iterClust", "version": "1.24.0", "sha256": "0k2hcc7g4ynd9jrk8f286y6gwc4bfs4bnfs8qpj2i8zamwdaldng", "depends": ["Biobase", "cluster"], "broken": true }, "iteremoval": { "name": "iteremoval", "version": "1.15.1", "sha256": "0bwl8lzxvf5azwyacv9x16l4kyi8l00xny2s83gp2kng5gyz8602", "depends": ["GenomicRanges", "ggplot2", "magrittr", "SummarizedExperiment"], "broken": true }, "jmosaics": { "name": "jmosaics", "version": "1.10.0", "sha256": "1q67ylrgc2abny2wxgsl1cni225inar1dhim0psrbrf5ik77kgmk", "depends": ["mosaics"], "broken": true }, "joda": { "name": "joda", "version": "1.18.0", "sha256": "0fjbxczwkn8f4p0h8dgi3vfn4qf9a650wmp01q20j7f0jsmmb06x", "depends": ["RBGL", "bgmm"], "broken": true }, "lapmix": { "name": "lapmix", "version": "1.72.0", "sha256": "19bhb7654h8pivsf3qxv518zp02ijbvlhkb4d93nyanns3g7zqas", "depends": ["Biobase"], "broken": true }, "logitT": { "name": "logitT", "version": "1.28.0", "sha256": "1qbimjjl5xv5h30r74bd86dg10djajb01qav6gp95l6f59fx2j1q", "depends": ["affy"], "broken": true }, "lol": { "name": "lol", "version": "1.18.0", "sha256": "0dc3ga7yalzfngh3y33sa4bchhbxgndkls3vdxh4yzcsdvk60i1f", "depends": ["Matrix", "penalized"], "broken": true }, "mAPKL": { "name": "mAPKL", "version": "1.2.0", "sha256": "1k1yxxj6371sagiy63fl1dh8d71cqg6gvx8pkjy3ahp1hbh45b6l", "depends": ["AnnotationDbi", "Biobase", "apcluster", "clusterSim", "e1071", "igraph", "limma", "multtest", "parmigene", "reactome_db"], "broken": true }, "mQTL_NMR": { "name": "mQTL.NMR", "version": "1.4.0", "sha256": "0flb1lqsq7ldicidag20icnhmds2qr85yrbjsv4h06klggq2vjvg", "depends": ["MASS", "outliers", "qtl"], "broken": true }, "maanova": { "name": "maanova", "version": "1.40.0", "sha256": "112hbyfw18dshshsmbaylwra169w6bbwwqql3d96s0in1fl20mdl", "depends": ["Biobase"], "broken": true }, "macat": { "name": "macat", "version": "1.44.1", "sha256": "061y6a1q7c9r9a01hy6l86wc085f530y7hjw7asx506cf91ifwdk", "depends": ["Biobase", "annotate"], "broken": true }, "maigesPack": { "name": "maigesPack", "version": "1.34.0", "sha256": "08pszyq03f1vjgirq0zcv31m4c0acdbfh622qiw0x0w1gz6plm0g", "depends": ["convert", "graph", "limma", "marray"], "broken": true }, "manta": { "name": "manta", "version": "1.16.0", "sha256": "0j6zll7b1qqdnydg59hywargw6bivry3cx5m2wpj79wn673kib3c", "depends": ["Hmisc", "caroline", "edgeR"], "broken": true }, "mbOmic": { "name": "mbOmic", "version": "1.3.0", "sha256": "079qs5apyqli7h16c6drmhibmc356rnllxks5ddfnnq7hdzmhdbw", "depends": ["cluster", "clusterSim", "data_table", "doParallel", "igraph", "psych", "visNetwork", "WGCNA"], "broken": true }, "mcaGUI": { "name": "mcaGUI", "version": "1.18.0", "sha256": "0rxhs059z0l6lal33m78hkp73k46c2pdy0nn5lxwxr590fglvh0f", "depends": ["MASS", "OTUbase", "bpca", "foreign", "lattice", "proto", "vegan"], "broken": true }, "mdgsa": { "name": "mdgsa", "version": "1.2.0", "sha256": "05lqj7d4464z976w4rvnzpv1abihq1fpxhcl2zyg5izwqpq6ga9r", "depends": ["AnnotationDbi", "DBI", "GO_db", "KEGG_db", "Matrix", "cluster"], "broken": true }, "metaArray": { "name": "metaArray", "version": "1.48.0", "sha256": "1zx9ymjqh851r33jv7fpyy4319fqi2kgjgxxbgpq1xl6cfkglr4h", "depends": ["Biobase", "MergeMaid"], "broken": true }, "metaX": { "name": "metaX", "version": "1.0.3", "sha256": "1v4519spcgvc2kc1cah5gmfjnx09zlam8p8d8m6wkw0ba600vv7b", "depends": ["BBmisc", "CAMERA", "DiffCorr", "Nozzle_R1", "RColorBrewer", "RCurl", "SSPA", "VennDiagram", "ape", "boot", "bootstrap", "caret", "data_table", "doParallel", "dplyr", "faahKO", "ggplot2", "igraph", "impute", "lattice", "missForest", "pROC", "pcaMethods", "pheatmap", "pls", "plyr", "preprocessCore", "reshape2", "scatterplot3d", "stringr", "vsn", "xcms"], "broken": true }, "metagene": { "name": "metagene", "version": "2.2.1", "sha256": "1l0zfhk4gnm3gvy24igismpb3j3m6vh4mb4q41cfrpkmxn2zlvaq", "depends": ["BiocParallel", "DBChIP", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "R6", "Rsamtools", "ggplot2", "gplots", "rtracklayer"], "broken": true }, "metagenomeFeatures": { "name": "metagenomeFeatures", "version": "1.0.0", "sha256": "1lbb505s976j2jxxi7snhd1yahcs0ca9qnicq12b5jmp3ki1br9k", "depends": ["Biobase", "Biostrings", "RSQLite", "ShortRead", "dplyr", "lattice", "lazyeval", "magrittr", "stringr"], "broken": true }, "metaseqR": { "name": "metaseqR", "version": "1.10.0", "sha256": "1gy5ywrxqwd8lizbj9lk6qck6zwk670j5y2f0ayz6xvkki4vab97", "depends": ["DESeq", "EDASeq", "NBPSeq", "NOISeq", "baySeq", "biomaRt", "brew", "corrplot", "edgeR", "gplots", "limma", "log4r", "qvalue", "rjson", "vsn"], "broken": true }, "metavizr": { "name": "metavizr", "version": "1.21.0", "sha256": "1d88f854sn5m2pklsyvkmq05yzjanxlnkz5gpzban62qq1mpvims", "depends": ["Biobase", "data_table", "digest", "epivizr", "epivizrData", "epivizrServer", "epivizrStandalone", "GenomeInfoDb", "httr", "metagenomeSeq", "phyloseq", "vegan"], "broken": true }, "methVisual": { "name": "methVisual", "version": "1.22.0", "sha256": "1kcqhlv0lmr7wlkxjl9qqv2676pwna3i4w5xpm4inwgcb892zgjm", "depends": ["Biostrings", "IRanges", "ca", "gridBase", "gsubfn", "plotrix", "sqldf"], "broken": true }, "methyAnalysis": { "name": "methyAnalysis", "version": "1.12.2", "sha256": "0m4qx7q1zm3g4m8kwjz7nvf93891bmbvac0n8wpgniap669af0yk", "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "VariantAnnotation", "annotate", "biomaRt", "genefilter", "genoset", "lumi", "methylumi", "org_Hs_eg_db", "rtracklayer"], "broken": true }, "miRmine": { "name": "miRmine", "version": "1.22.0", "sha256": "1d0ni3lavpiv2qzwlmrsjym75cip3i9q1bg9rwa04h61rz2smylg", "depends": ["SummarizedExperiment"], "broken": true }, "microbiomeMarker": { "name": "microbiomeMarker", "version": "1.12.2", "sha256": "0fkm2sqqsaa8kkdyp0j3zwx8lijgkgk4s45sir3s37an9yai2bp4", "depends": ["ALDEx2", "ANCOMBC", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "ComplexHeatmap", "DESeq2", "IRanges", "MASS", "S4Vectors", "biomformat", "caret", "coin", "dplyr", "edgeR", "ggplot2", "ggsignif", "ggtree", "limma", "magrittr", "metagenomeSeq", "multtest", "pROC", "patchwork", "phyloseq", "plotROC", "purrr", "rlang", "tibble", "tidyr", "tidytree", "vegan", "yaml"], "broken": true }, "mitoODE": { "name": "mitoODE", "version": "1.8.0", "sha256": "1rbxppzwmlrfyzcsa5b0biqm79qyv9662dh16zzp3frz56325kzy", "depends": ["KernSmooth", "MASS", "minpack_lm", "mitoODEdata"], "broken": true }, "mmnet": { "name": "mmnet", "version": "1.8.1", "sha256": "0ppcy11xnn593xig8gwz79vsbkdi3f5aai58zdhr59w52y2dafia", "depends": ["Biobase", "KEGGREST", "Matrix", "RCurl", "RJSONIO", "XML", "flexmix", "ggplot2", "igraph", "plyr", "reshape2", "stringr"], "broken": true }, "motifRG": { "name": "motifRG", "version": "1.14.0", "sha256": "1v9zm5629k2lcqbbgw8bwflvbircyxkfavbkvmbd212kgwcng8vn", "depends": ["BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "Biostrings", "IRanges", "XVector", "seqLogo"], "broken": true }, "multiOmicsViz": { "name": "multiOmicsViz", "version": "1.24.0", "sha256": "129k094ml403w25k3kipzbavx78p14jxq40a8d733qyqp8mcnlrs", "depends": ["doParallel", "foreach", "SummarizedExperiment"], "broken": true }, "multiSight": { "name": "multiSight", "version": "1.7.0", "sha256": "1v2ml1qh250lidm5a0xw4b3xbxd2as86p703qn5s8m1xi6l89b9c", "depends": ["anyLib", "biosigner", "caret", "clusterProfiler", "config", "DESeq2", "dplyr", "DT", "easyPubMed", "enrichplot", "ggnewscale", "golem", "htmltools", "igraph", "infotheo", "metap", "mixOmics", "networkD3", "ppcor", "R6", "ReactomePA", "rmarkdown", "rWikiPathways", "shiny", "shinydashboard", "stringr"], "broken": true }, "mvGST": { "name": "mvGST", "version": "1.4.0", "sha256": "1yi8558lkqfrmxgighb5v8q12gwqlbs2ds610fgf8ggrdn84bzq8", "depends": ["AnnotationDbi", "GO_db", "GOstats", "Rgraphviz", "annotate", "gProfileR", "graph", "stringr", "topGO"], "broken": true }, "nanotatoR": { "name": "nanotatoR", "version": "1.18.0", "sha256": "1nnh4g4b7k6mp922pr52sxlrh6wvfyx7jhckmwrd12l1yjq010pb", "depends": ["AnnotationDbi", "curl", "dplyr", "GenomicRanges", "hash", "httr", "knitr", "openxlsx", "org_Hs_eg_db", "rentrez", "rlang", "stringr", "testthat", "tidyverse", "XML"], "broken": true }, "neaGUI": { "name": "neaGUI", "version": "1.8.0", "sha256": "1xms5k8zzbk31sj0f92rsqjv40vcqy89pmy8z3j0336iascqbx9l", "depends": ["hwriter"], "broken": true }, "nem": { "name": "nem", "version": "2.44.0", "sha256": "1bkq622jyrfn0v4wyw5ycxmri8kyils4wznsz26ki3awff34lq3h", "depends": ["RBGL", "RColorBrewer", "Rgraphviz", "boot", "e1071", "graph", "limma", "plotrix", "statmod"], "broken": true }, "netDx": { "name": "netDx", "version": "1.16.0", "sha256": "00ghcj5hzb06pi9aj2rdnasyqgqnvr9qjb0m6b0476yv2mx5x24k", "depends": ["BiocFileCache", "GenomeInfoDb", "GenomicRanges", "IRanges", "MultiAssayExperiment", "RColorBrewer", "ROCR", "Rtsne", "S4Vectors", "bigmemory", "combinat", "doParallel", "foreach", "ggplot2", "glmnet", "httr", "igraph", "plotrix", "pracma", "rappdirs", "reshape2"], "broken": true }, "netOmics": { "name": "netOmics", "version": "1.8.0", "sha256": "03nyjvcr2hldsfifj0dix1bc79z05i9x2hgc5z2g9hd1jyijljyd", "depends": ["AnnotationDbi", "dplyr", "ggplot2", "GO_db", "gprofiler2", "igraph", "magrittr", "minet", "purrr", "RandomWalkRestartMH", "tibble", "tidyr"], "broken": true }, "netZooR": { "name": "netZooR", "version": "1.10.0", "sha256": "11rq1lhxhwij6wik087wmnzk8aswhmmf3yzcpiljxbk8szsm8np7", "depends": ["AnnotationDbi", "Biobase", "GO_db", "GOstats", "MASS", "Matrix", "RCy3", "STRINGdb", "assertthat", "data_table", "doParallel", "dplyr", "foreach", "ggdendro", "ggplot2", "gplots", "igraph", "matrixStats", "matrixcalc", "nnet", "org_Hs_eg_db", "pandaR", "penalized", "reshape", "reshape2", "reticulate", "tidyr", "vegan", "viridisLite", "yarn"], "broken": true }, "netbenchmark": { "name": "netbenchmark", "version": "1.2.0", "sha256": "10s8xsisjp9sj9dl67bgn94ipm6a6kpqli3pvjdpxkmvjkg400kg", "depends": ["GeneNet", "Matrix", "Rcpp", "c3net", "corpcor", "fdrtool", "grndata", "minet", "pracma", "randomForest"], "broken": true }, "netbiov": { "name": "netbiov", "version": "1.4.0", "sha256": "1h3986kfi516xlw675cq901ls9v7rj5rr0ls5lny21wd439n2avf", "depends": ["igraph"], "broken": true }, "netboxr": { "name": "netboxr", "version": "1.9.0", "sha256": "1brnm60745s2axls4p6qcxipjjr3ph9ijg1q604fgm42rf6i7qzm", "depends": ["clusterProfiler", "data_table", "DT", "gplots", "igraph", "jsonlite", "plyr", "RColorBrewer"], "broken": true }, "networkBMA": { "name": "networkBMA", "version": "1.12.0", "sha256": "0zkf10iqiabsln1jxq0sypr43mrw6k82l3pdp5bg9kcv0bqqqy5k", "depends": ["BMA", "Rcpp", "RcppArmadillo", "RcppEigen"], "broken": true }, "nudge": { "name": "nudge", "version": "1.36.0", "sha256": "1px6hnda7hp7yx9imkl8xq8m772csd2qic0kq5bqwshk5qdvfhw7", "depends": [], "broken": true }, "oneChannelGUI": { "name": "oneChannelGUI", "version": "1.36.0", "sha256": "0r5y531y4niy9gh64n7nk8a0xcj8lyg36axhcjx116ycsqa00x5h", "depends": ["Biobase", "Biostrings", "IRanges", "Rsamtools", "affylmGUI", "chimera", "siggenes", "tkWidgets", "tkrplot"], "broken": true }, "oneSENSE": { "name": "oneSENSE", "version": "1.20.0", "sha256": "1lzb8i3frv3va2q28glwnjwszrynhky5y8fx10q4h52p2wqgc4v3", "depends": ["flowCore", "gplots", "plotly", "Rtsne", "scatterplot3d", "shiny", "shinyFiles", "webshot"], "broken": true }, "ontoCAT": { "name": "ontoCAT", "version": "1.22.0", "sha256": "03vy4210m31jzhhhbhw3ixhm1lji4qil2zp0ckmyh3xb8m8s8fzl", "depends": ["rJava"], "broken": true }, "openPrimeRui": { "name": "openPrimeRui", "version": "1.26.0", "sha256": "0w00ya6xb70am000hybrxgcq8bpd950w36n01v4l0pfmfcvqd9fa", "depends": ["DT", "openPrimeR", "rmarkdown", "shiny", "shinyBS", "shinyjs"], "broken": true }, "pareg": { "name": "pareg", "version": "1.8.0", "sha256": "1b9vvn1ppw1vbfmkzkbd6b01pkqnsknbrjv1js983dpjv23x6xlb", "depends": ["DOSE", "Matrix", "basilisk", "devtools", "doFuture", "doRNG", "dplyr", "foreach", "future", "ggplot2", "ggraph", "ggrepel", "glue", "hms", "igraph", "keras", "logger", "magrittr", "nloptr", "progress", "proxy", "purrr", "reticulate", "rlang", "stringr", "tensorflow", "tfprobability", "tibble", "tidygraph", "tidyr"], "broken": true }, "pathVar": { "name": "pathVar", "version": "1.0.1", "sha256": "1ixraifr8d86m9rdg38d6kfzmgghjxasgi3abb1i8knjyfwrc05v", "depends": ["EMT", "Matching", "data_table", "ggplot2", "gridExtra", "mclust"], "broken": true }, "paxtoolsr": { "name": "paxtoolsr", "version": "1.4.6", "sha256": "170gm5qxlsz2dv249q16shpj0xm9y7rp3rpn9ij6r2c5d3xn8i21", "depends": ["R_utils", "XML", "data_table", "httr", "igraph", "plyr", "rJava", "rjson"], "broken": true }, "pcaGoPromoter": { "name": "pcaGoPromoter", "version": "1.14.0", "sha256": "1w0cpakxlm8dx6z3j844xmkz3dawiaschrjcjlkqjv9ay8vfkhz8", "depends": ["AnnotationDbi", "Biostrings", "ellipse"], "broken": true }, "pcot2": { "name": "pcot2", "version": "1.38.0", "sha256": "1ycsbry5srf1msq4vcvv0q34lgzkwadh7k1pgwv963i567i4lx3b", "depends": ["Biobase", "amap"], "broken": true }, "pcxn": { "name": "pcxn", "version": "2.26.0", "sha256": "13gahdsvz7ss3chcvqmdyrnw31rcgiplqg7awrn930drwljlimqk", "depends": ["pcxnData", "pheatmap"], "broken": true }, "pdmclass": { "name": "pdmclass", "version": "1.42.0", "sha256": "1f4zrxbyk49hm0cxp0g1786cwc7g1k5z6v3hn2z66m7rbapz8afy", "depends": ["Biobase", "fibroEset", "mda"], "broken": true }, "perturbatr": { "name": "perturbatr", "version": "1.13.0", "sha256": "0ssk8cr42hibn917s2z2nzcdan54c7xiydypbi8f3g4w68q4ly31", "depends": ["assertthat", "diffusr", "doParallel", "dplyr", "foreach", "formula_tools", "ggplot2", "igraph", "lazyeval", "lme4", "magrittr", "rlang", "scales", "tibble", "tidyr"], "broken": true }, "phemd": { "name": "phemd", "version": "1.18.0", "sha256": "174jp26insq2mwf9yw9bls4i9b2a8vccfkrg2h1dzvyyk513bi83", "depends": ["Biobase", "BiocGenerics", "cluster", "cowplot", "destiny", "ggplot2", "igraph", "maptree", "monocle", "phateR", "pheatmap", "pracma", "RANN", "RColorBrewer", "reticulate", "Rtsne", "S4Vectors", "scatterplot3d", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "transport", "VGAM"], "broken": true }, "phenoDist": { "name": "phenoDist", "version": "1.18.0", "sha256": "0kjsdgvr5kmrnn7mjzphk5r6irgjv5cfgmrd4yddprbmmln39avn", "depends": ["e1071", "imageHTS"], "broken": true }, "pint": { "name": "pint", "version": "1.20.0", "sha256": "19q21b3zdn4adx49zn88z69xz3mqza58xdhig3zicn9s0g21bfz4", "depends": ["Matrix", "mvtnorm"], "broken": true }, "pkgDepTools": { "name": "pkgDepTools", "version": "1.36.0", "sha256": "1v2fsax49wklwdmgxp9pjyp18cbj2rsg7yd68mwr2amlihgvmsp1", "depends": ["RBGL", "graph"], "broken": true }, "plateCore": { "name": "plateCore", "version": "1.28.0", "sha256": "1v7shvjnav930grswbixj8fyabmamsgry5g5is3sf9ymp9r8gh5x", "depends": ["Biobase", "MASS", "flowCore", "flowStats", "flowViz", "lattice", "latticeExtra", "robustbase"], "broken": true }, "plethy": { "name": "plethy", "version": "1.8.0", "sha256": "1skaqws1yb8n8li4daprq4x8vrbyykm3fk6pzwx7iyr3nf2r2zz5", "depends": ["Biobase", "BiocGenerics", "DBI", "IRanges", "RColorBrewer", "RSQLite", "S4Vectors", "Streamer", "ggplot2", "plyr", "reshape2"], "broken": true }, "plrs": { "name": "plrs", "version": "1.10.0", "sha256": "1f2dlgcbpfrn5za2z7nf1y8jzrcb5hzb3gix18nyqmz9syg57zha", "depends": ["Biobase", "BiocGenerics", "CGHbase", "Rcsdp", "ic_infer", "marray", "quadprog"], "broken": true }, "plw": { "name": "plw", "version": "1.30.0", "sha256": "190bccvxhdgp3ah9vzdpjddb33ck38r5x4gw1f8vwxh0mw79vf9c", "depends": ["MASS", "affy"], "broken": true }, "polyester": { "name": "polyester", "version": "1.6.0", "sha256": "0if2rbgbfc3ghz5mnmpmpv6rq63qjm3l16gmlr493vfrpxdzclnv", "depends": ["Biostrings", "IRanges", "S4Vectors", "limma", "logspline"], "broken": true }, "ppiStats": { "name": "ppiStats", "version": "1.36.0", "sha256": "1s5xv565w924g71qaxgmhfszrkqs3arzi8l0vzcz446r2pgm6d32", "depends": ["Biobase", "Category", "RColorBrewer", "ScISI", "graph", "lattice", "ppiData"], "broken": true }, "prada": { "name": "prada", "version": "1.46.0", "sha256": "0ak21586bbkbpwji1pcbr44dlwyhslscrqm2y172310xbxm0sqbg", "depends": ["Biobase", "BiocGenerics", "MASS", "RColorBrewer", "rrcov"], "broken": true }, "predictionet": { "name": "predictionet", "version": "1.16.0", "sha256": "1q7nl11kvh2rl5rzb4qnq5ckdrdkna0arfnjmki35lr8hyh65id0", "depends": ["MASS", "RBGL", "igraph", "penalized"], "broken": true }, "proBatch": { "name": "proBatch", "version": "1.14.0", "sha256": "079dh61v1dmsasrh5sn6sn1rgi34mavxa1sc1y8x6wqjwabm4w1j", "depends": ["Biobase", "corrplot", "data_table", "dplyr", "ggfortify", "ggplot2", "lazyeval", "lubridate", "magrittr", "pheatmap", "preprocessCore", "purrr", "pvca", "RColorBrewer", "reshape2", "rlang", "scales", "sva", "tibble", "tidyr", "viridis", "wesanderson", "WGCNA"], "broken": true }, "proFIA": { "name": "proFIA", "version": "1.23.0", "sha256": "0y08vj401f45dvgxjwjx94hvd0rk1wljk8n1irpkdafg24gv4fvj", "depends": ["Biobase", "BiocParallel", "minpack_lm", "missForest", "pracma", "ropls", "xcms"], "broken": true }, "prot2D": { "name": "prot2D", "version": "1.8.0", "sha256": "0pmsl550wvxnqx5zbj8b6lhvlb2bcmvi3xxx66x8r1sz3cdy3l7h", "depends": ["Biobase", "MASS", "Mulcom", "fdrtool", "impute", "limma", "qvalue", "samr", "st"], "broken": true }, "proteasy": { "name": "proteasy", "version": "1.2.0", "sha256": "1mfk69k44krdj4wp6xpil391j9jrppyx1crvra525p8hahzc2d5m", "depends": ["AnnotationFilter", "data_table", "EnsDb_Hsapiens_v86", "EnsDb_Mmusculus_v79", "EnsDb_Rnorvegicus_v79", "ensembldb", "Rcpi", "stringr"], "broken": true }, "proteoQC": { "name": "proteoQC", "version": "1.6.0", "sha256": "15raykmw19k4yn4jppw4lqwgarr8b7sfsvhcif49xvw7k1dwj5ys", "depends": ["MSnbase", "Nozzle_R1", "Rcpp", "VennDiagram", "XML", "ggplot2", "plyr", "rTANDEM", "reshape2", "seqinr"], "broken": true }, "psygenet2r": { "name": "psygenet2r", "version": "1.36.0", "sha256": "1khjid5lkkn5qpnk9adw1in4km41q067mj5r5yqs2iz5hv4vx6xv", "depends": ["BgeeDB", "Biobase", "GO_db", "RCurl", "biomaRt", "ggplot2", "igraph", "labeling", "reshape2", "stringr", "topGO"], "broken": true }, "pulsedSilac": { "name": "pulsedSilac", "version": "1.9.1", "sha256": "1zb8xzs9h4rcrnmsfvrwb1qixn3jbnzxdwqgdrb82hgmxabmajlb", "depends": ["cowplot", "ggplot2", "ggridges", "MuMIn", "R_utils", "robustbase", "S4Vectors", "SummarizedExperiment", "UpSetR"], "broken": true }, "pwOmics": { "name": "pwOmics", "version": "1.2.0", "sha256": "0vlr71mhch716xl2i0366pxjkawci0g2imvfhsqinv5gd92m6hpq", "depends": ["AnnotationDbi", "AnnotationHub", "Biobase", "BiocGenerics", "GenomicRanges", "STRINGdb", "biomaRt", "data_table", "gplots", "igraph", "rBiopaxParser"], "broken": true }, "pwrEWAS": { "name": "pwrEWAS", "version": "1.14.0", "sha256": "1913h2syad9mfspxjvmrwm0mrcklbcl89lj04rn5x0xgfk8rk58a", "depends": ["abind", "BiocManager", "CpGassoc", "doParallel", "doSNOW", "foreach", "genefilter", "ggplot2", "limma", "pwrEWAS_data", "shiny", "shinyBS", "shinyWidgets", "truncnorm"], "broken": true }, "qrqc": { "name": "qrqc", "version": "1.24.0", "sha256": "0850frx6fg9py2laav0yqavl9ckbn6y475xm9r6gxvyzp63smzdg", "depends": ["Biostrings", "Rsamtools", "biovizBase", "brew", "ggplot2", "plyr", "reshape", "testthat", "xtable"], "broken": true }, "rDGIdb": { "name": "rDGIdb", "version": "1.30.0", "sha256": "1v96nj1ffmg1678p7rspcqsnqvwcssv96jcyqqbb8v8sryflwmi5", "depends": ["httr", "jsonlite"], "broken": true }, "rHVDM": { "name": "rHVDM", "version": "1.36.0", "sha256": "0k1gccnac59q54y2nypzgip2srs5yg3v2hhrz86ps50p2lx4pqd2", "depends": ["Biobase", "R2HTML", "affy", "minpack_lm"], "broken": true }, "rMAT": { "name": "rMAT", "version": "3.20.0", "sha256": "0dq4ipz1j6qai8q8z038hjb5j0w67gp7449vj8psgca2854gxa7s", "depends": ["Biobase", "BiocGenerics", "IRanges", "affxparser"], "broken": true }, "rSFFreader": { "name": "rSFFreader", "version": "0.18.0", "sha256": "0z2lkjbs3svx1b9zr4smjwrcd9xzxhfp98428vzaqq0k79h1v666", "depends": ["Biostrings", "IRanges", "S4Vectors", "ShortRead", "XVector"], "broken": true }, "rTANDEM": { "name": "rTANDEM", "version": "1.10.0", "sha256": "1dmaqdjfmjkkrddf666hpp95s7s6x0ssinx9aybl6952ylfjgcd1", "depends": ["Rcpp", "XML", "data_table"], "broken": true }, "rama": { "name": "rama", "version": "1.44.0", "sha256": "0nka6a2dk7jn4lk0i2p91hxwdgpny6y3j4dz709crrxlz3xjqflm", "depends": [], "broken": true }, "reb": { "name": "reb", "version": "1.48.0", "sha256": "1bxijf91vdr6088459r29kvy691bjbscy170pc0739iqbg7z80zm", "depends": ["Biobase", "idiogram"], "broken": true }, "restfulSE": { "name": "restfulSE", "version": "1.24.0", "sha256": "0i40yfvynxy34jfkvzyvjwvxf89zi4pvy9m9i0bk93l17gyhnjyl", "depends": ["AnnotationDbi", "AnnotationHub", "bigrquery", "Biobase", "DBI", "DelayedArray", "dplyr", "ExperimentHub", "GO_db", "magrittr", "reshape2", "rhdf5client", "rlang", "S4Vectors", "SummarizedExperiment"], "broken": true }, "rnaSeqMap": { "name": "rnaSeqMap", "version": "2.28.0", "sha256": "0mfcy7l31g5z5yv12sv9imaf19p9vawnk7cqcm50x2sm032r8n7f", "depends": ["Biobase", "DBI", "DESeq", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "edgeR"], "broken": true }, "sRAP": { "name": "sRAP", "version": "1.10.0", "sha256": "080s88l3a2fbgqnc8sy41kwzkm6skjazkirqini7n6xqcsqb9lih", "depends": ["ROCR", "WriteXLS", "gplots", "pls", "qvalue"], "broken": true }, "sapFinder": { "name": "sapFinder", "version": "1.8.0", "sha256": "12a0wcjxcz77b06bymhqcj5wxzm478mlj9vcvbbqhdfvj7214hy9", "depends": ["Rcpp", "pheatmap", "rTANDEM"], "broken": true }, "saps": { "name": "saps", "version": "2.2.0", "sha256": "11v7nxlcnkslxl0giv3y2naxpfsmqmrj6b4y2g6zbp48zml45jgl", "depends": ["piano", "reshape2", "survcomp", "survival"], "broken": true }, "savR": { "name": "savR", "version": "1.8.0", "sha256": "1vxxmzr8k6fn9fqr0pbfvccqq30d8w3fwjcr5x0bh1d77mzgf9n1", "depends": ["XML", "ggplot2", "gridExtra", "reshape2", "scales"], "broken": true }, "sbgr": { "name": "sbgr", "version": "1.0.0", "sha256": "0bvvxd0c4k4mmwkcb9w02i2kb6vwlq84w8vfqiamnwjy2vgjgka9", "depends": ["httr", "jsonlite", "objectProperties"], "broken": true }, "scAlign": { "name": "scAlign", "version": "1.12.0", "sha256": "1mlhxwsfrmhysa5mcyx7vf2jn49snf41yb7xqmyi40wilj9h8qlb", "depends": ["FNN", "ggplot2", "irlba", "purrr", "Rtsne", "Seurat", "SingleCellExperiment", "tensorflow"], "broken": true }, "scClassifR": { "name": "scClassifR", "version": "1.2.0", "sha256": "0p9l9q5ina0axrqvqn1y5wkfqi0nacxm3nm6ny34j53znv07b2zz", "depends": ["ape", "caret", "data_tree", "dplyr", "e1071", "ggplot2", "kernlab", "pROC", "ROCR", "Seurat", "SingleCellExperiment", "SummarizedExperiment"], "broken": true }, "scMAGeCK": { "name": "scMAGeCK", "version": "1.9.1", "sha256": "1i6l8jxrd66aqk3m9212wsi8jqklvs0agsqrllvf9mrh16js4vby", "depends": ["ggplot2", "Seurat"], "broken": true }, "scsR": { "name": "scsR", "version": "1.6.0", "sha256": "0g1vgx8wrdwbhlzmf0a11fg5jnbkvz402h8qj48vj4bq8j202bc1", "depends": ["BiocGenerics", "Biostrings", "IRanges", "RColorBrewer", "STRINGdb", "ggplot2", "hash", "plyr", "sqldf"], "broken": true }, "seqCNA": { "name": "seqCNA", "version": "1.16.0", "sha256": "1wq92wszv0x99l52lm3k0zc2ffin1sp78xlyfabxpwi1v0yrkifl", "depends": ["GLAD", "adehabitatLT", "doSNOW", "seqCNA_annot"], "broken": true }, "seqbias": { "name": "seqbias", "version": "1.18.0", "sha256": "1wwskcbl3wd8gl63jl4wl0xwzj8kbwbc8xhp12z3xximngkk7dgd", "depends": ["Biostrings", "GenomicRanges", "Rsamtools", "zlibbioc"], "broken": true }, "seqplots": { "name": "seqplots", "version": "1.8.1", "sha256": "0anv2048m5zp2ijfzk79avcwzp662gw0y58j7nafha21j5s2qyhm", "depends": ["BSgenome", "Biostrings", "DBI", "DT", "GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "RSQLite", "S4Vectors", "class", "digest", "fields", "ggplot2", "gridExtra", "jsonlite", "kohonen", "plotrix", "reshape2", "rtracklayer", "shiny"], "broken": true }, "shinyTANDEM": { "name": "shinyTANDEM", "version": "1.8.0", "sha256": "0dkgwfynznpq2q55d83w4x0nmal3dkgzxi1jpdcsasqlhsyqvmvx", "depends": ["mixtools", "rTANDEM", "shiny", "xtable"], "broken": true }, "sigPathway": { "name": "sigPathway", "version": "1.38.0", "sha256": "126cyw88d6rxp3bzdqsmm2v0kvhn650qmi4zcs9v50n0hhwyrxrf", "depends": [], "broken": true }, "sigaR": { "name": "sigaR", "version": "1.14.0", "sha256": "07ip468liyg9b6q9izd1wdp29p9f2icfs01nf0il4gc76h6d0rr5", "depends": ["Biobase", "CGHbase", "MASS", "corpcor", "igraph", "marray", "mvtnorm", "penalized", "quadprog", "snowfall"], "broken": true }, "simpleaffy": { "name": "simpleaffy", "version": "2.46.0", "sha256": "1x3f7hm7w44yarq4irv791330zfamhsqqwnqz8xfwrpvjrkv6avn", "depends": ["Biobase", "BiocGenerics", "affy", "gcrma", "genefilter"], "broken": true }, "simulatorZ": { "name": "simulatorZ", "version": "1.4.0", "sha256": "1sypvrwq6ay7lzmb9cmpix1zgzafzryvf4my5jky846bcpam91qj", "depends": ["Biobase", "BiocGenerics", "GenomicRanges", "Hmisc", "IRanges", "S4Vectors", "SummarizedExperiment", "gbm", "survival"], "broken": true }, "single": { "name": "single", "version": "1.7.0", "sha256": "0h7h9m4xr65nayr707jvjnbic1q4z0hsghw5i3pfpz2n6p9pb8s8", "depends": ["BiocGenerics", "Biostrings", "GenomicAlignments", "IRanges", "Rsamtools", "dplyr", "reshape2", "rlang", "stringr", "tidyr"], "broken": true }, "slinky": { "name": "slinky", "version": "1.12.0", "sha256": "05ywydvyz3jnzbhabhz1sd61hpy9nb22512zpbi48mv5wic1sv3v", "depends": ["curl", "dplyr", "foreach", "httr", "jsonlite", "readr", "rhdf5", "SummarizedExperiment", "tidyr"], "broken": true }, "snapCGH": { "name": "snapCGH", "version": "1.40.0", "sha256": "0fjqp0qhwk041pgwqp3av5ihkf4xb9li6zy6gmvk24hlj8sm600z", "depends": ["DNAcopy", "GLAD", "aCGH", "cluster", "limma", "tilingArray"], "broken": true }, "sojourner": { "name": "sojourner", "version": "1.11.0", "sha256": "1s0iqzn65s9g4yymy059z122i9wvgkcb5718snzxhj7mkqjzwhhc", "depends": ["dplyr", "EBImage", "fitdistrplus", "ggplot2", "gridExtra", "lattice", "MASS", "mclust", "minpack_lm", "mixtools", "mltools", "nls2", "pixmap", "plyr", "R_matlab", "Rcpp", "reshape2", "rlang", "scales", "shiny", "shinyjs", "sp", "truncnorm"], "broken": true }, "spade": { "name": "spade", "version": "1.18.2", "sha256": "0m2784x2ysp4mc7m8n8scpr1h38m3p9glcc5jd6cix55bh3yzykk", "depends": ["Biobase", "flowCore", "igraph"], "broken": true }, "sparseDOSSA": { "name": "sparseDOSSA", "version": "1.24.0", "sha256": "1xy9kd5a9vilwkgr4xw6lcdwgwykg7q7kildpfw4gqymd1frnjp6", "depends": ["MASS", "MCMCpack", "optparse", "tmvtnorm"], "broken": true }, "spliceR": { "name": "spliceR", "version": "1.12.0", "sha256": "0r5j0ibl2ccsxb7rr2fxw4b07wbdiyfndxkl4pgd9h0ks4qyhyjy", "depends": ["GenomicRanges", "IRanges", "RColorBrewer", "VennDiagram", "cummeRbund", "plyr", "rtracklayer"], "broken": true }, "spliceSites": { "name": "spliceSites", "version": "1.8.3", "sha256": "1jifh0nbqjhrc07jfc50hfk4wn1hv3a863rbr3fnqlg9rwg044w7", "depends": ["Biobase", "BiocGenerics", "Biostrings", "IRanges", "doBy", "seqLogo"], "broken": true }, "splicegear": { "name": "splicegear", "version": "1.42.0", "sha256": "1g2fqql1wqzwz1vx5cq03ckld0gccqk6rv9l99xsaa8mhf0rn1qa", "depends": ["Biobase", "XML", "annotate"], "broken": true }, "spotSegmentation": { "name": "spotSegmentation", "version": "1.44.0", "sha256": "074nzh18pj6dpk9bqh8id0j2vpaxvhi2ddrz6hnza381wzdgxdr3", "depends": ["mclust"], "broken": true }, "sscore": { "name": "sscore", "version": "1.42.0", "sha256": "0h86crb241vmaczp76wz4zv9ni1snmlkrdi1md3hgq1hqxnn9gzs", "depends": ["affy", "affyio"], "broken": true }, "staRank": { "name": "staRank", "version": "1.12.0", "sha256": "1vgc3mhxyhrgwkapnqx4061l9l0nyc012508hma14xbxml3f76sg", "depends": ["cellHTS2"], "broken": true }, "stepwiseCM": { "name": "stepwiseCM", "version": "1.16.0", "sha256": "1ss79yr75kw7fsd8ihpivj9k5v32zxr3ymkl6prba0nyxdj5wyz9", "depends": ["Biobase", "e1071", "glmpath", "pamr", "penalized", "randomForest", "snowfall", "tspair"], "broken": true }, "supraHex": { "name": "supraHex", "version": "1.8.0", "sha256": "1g2zcarzi805y2933pyjdgg7l9imbhdf4pjhyr8bir0149li98cy", "depends": ["MASS", "ape", "hexbin"], "broken": true }, "tofsims": { "name": "tofsims", "version": "1.22.0", "sha256": "0da4843wbcr821yp8z3z4vd81qpm2lblckgd01fm89lmwj393z65", "depends": ["ALS", "alsace", "KernSmooth", "ProtGenerics", "Rcpp", "RcppArmadillo", "signal"], "broken": true }, "traviz": { "name": "traviz", "version": "1.10.0", "sha256": "1jjdfl8xvzlr31w74j12s5pdg5b1yylg1i30n804p9mqyx11g5sc", "depends": ["Biobase", "RColorBrewer", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "mgcv", "princurve", "rgl", "slingshot", "viridis"], "broken": true }, "trena": { "name": "trena", "version": "1.22.2", "sha256": "1xjhqm2g53kgcnnqhs5l3vn525h7amaz4hvsskjp5zb0gkfpiwh1", "depends": ["AnnotationDbi", "biomaRt", "Biostrings", "BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "BSgenome_Hsapiens_UCSC_hg38", "BSgenome_Mmusculus_UCSC_mm10", "DBI", "GenomicRanges", "glmnet", "lassopv", "MotifDb", "org_Hs_eg_db", "randomForest", "RMySQL", "RPostgreSQL", "RSQLite", "SNPlocs_Hsapiens_dbSNP150_GRCh38", "WGCNA", "xgboost"], "broken": true }, "triform": { "name": "triform", "version": "1.12.0", "sha256": "0pqfz6msalr2264iwi2hzam2sv8yl4fy1ri72pff5gh14rbxgiml", "depends": ["BiocGenerics", "IRanges", "yaml"], "broken": true }, "tscR": { "name": "tscR", "version": "1.11.0", "sha256": "19jpmyb6dly7l0418c1z0dlb936wjh6nwkb0mvk13ym19qgv1my7", "depends": ["class", "cluster", "dplyr", "dtw", "GenomicRanges", "ggplot2", "gridExtra", "IRanges", "knitr", "latex2exp", "prettydoc", "RColorBrewer", "rmarkdown", "S4Vectors", "SummarizedExperiment"], "broken": true }, "tspair": { "name": "tspair", "version": "1.28.0", "sha256": "0m083g5z77n7dd4lnbhvbwjkykh7a4pl4v8j7ipr5w7f9dhdjk33", "depends": ["Biobase"], "broken": true }, "waveTiling": { "name": "waveTiling", "version": "1.12.0", "sha256": "0j866mgxj44mv4wp0yqnav83w8pfb47lmjhp1y0qqvxc6q9k80g8", "depends": ["Biobase", "Biostrings", "GenomeGraphs", "GenomicRanges", "IRanges", "affy", "oligo", "oligoClasses", "preprocessCore", "waveslim"], "broken": true }, "xps": { "name": "xps", "version": "1.30.0", "sha256": "0wh98fsj3j368bxk4wa7rjd3acwl04r1dfiy13a89zv1fzv3wvky", "depends": [], "broken": true }, "yaqcaffy": { "name": "yaqcaffy", "version": "1.30.0", "sha256": "1pj2ksqbj7dlc76s6qagi7iq35wa83gx5cp0hm42w3bj7mxprjbi", "depends": ["simpleaffy"], "broken": true } } }