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depot/pkgs/development/r-modules/bioc-packages.json
Luke Granger-Brown 57725ef3ec Squashed 'third_party/nixpkgs/' content from commit 76612b17c0ce 
git-subtree-dir: third_party/nixpkgs
git-subtree-split: 76612b17c0ce71689921ca12d9ffdc9c23ce40b2
2024-11-10 23:59:47 +00:00

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{
"extraArgs": {
"biocVersion": "3.19"
},
"packages": {
"ABSSeq": {
"name": "ABSSeq",
"version": "1.58.0",
"sha256": "0zqb2w055x4whgl3mljarsnps6lkz90fwlx2lnirbnrgmlnalwjz",
"depends": ["limma", "locfit"]
},
"ABarray": {
"name": "ABarray",
"version": "1.72.0",
"sha256": "1kfqq4df55pxl7gnwf24aaryxijym4gzqfjyif28arlbjci9hlv6",
"depends": ["Biobase", "multtest"]
},
"ACE": {
"name": "ACE",
"version": "1.22.0",
"sha256": "1gpn9z09cfcy2mj7m32xfb2bjjwl01g9qn9nqaivmqbi4k6icrr8",
"depends": ["Biobase", "GenomicRanges", "QDNAseq", "ggplot2"]
},
"ACME": {
"name": "ACME",
"version": "2.60.0",
"sha256": "0jak83dlavhczaa2nqk5g2l0h4grnc9v24bg6v9mjfn6bqhl1s7j",
"depends": ["Biobase", "BiocGenerics"]
},
"ADAM": {
"name": "ADAM",
"version": "1.20.0",
"sha256": "0z0rmpwfhd8p6c4zscviwsningsm740r3pb95cl8brasfdg1kl3v",
"depends": ["DT", "GO_db", "KEGGREST", "Rcpp", "SummarizedExperiment", "dplyr", "knitr", "pbapply", "stringr"]
},
"ADAMgui": {
"name": "ADAMgui",
"version": "1.20.0",
"sha256": "08kxkb6hgbw7l9dv1wn3jfdkc0sizqdgmjkrzpq73q7rf0p4248g",
"depends": ["ADAM", "DT", "GO_db", "RColorBrewer", "colorRamps", "data_table", "dplyr", "ggplot2", "ggpubr", "ggrepel", "ggsignif", "gridExtra", "knitr", "reshape2", "shiny", "shinyjs", "stringi", "stringr", "testthat", "varhandle"]
},
"ADImpute": {
"name": "ADImpute",
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"depends": ["BiocParallel", "DrImpute", "MASS", "Matrix", "S4Vectors", "SAVER", "SingleCellExperiment", "SummarizedExperiment", "checkmate", "data_table", "kernlab", "rsvd"]
},
"ADaCGH2": {
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"sha256": "1j9dn0xw8mdfvi2ccm1d5j9q740wb89wqi6715n6jy3dljlc8irz",
"depends": ["DNAcopy", "GLAD", "aCGH", "bit", "cluster", "ff", "tilingArray", "waveslim"]
},
"AGDEX": {
"name": "AGDEX",
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"depends": ["Biobase", "GSEABase"]
},
"AHMassBank": {
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"depends": ["AnnotationHubData"]
},
"AIMS": {
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"depends": ["Biobase", "e1071"]
},
"ALDEx2": {
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"depends": ["BiocParallel", "GenomicRanges", "IRanges", "Rfast", "S4Vectors", "SummarizedExperiment", "directlabels", "lattice", "latticeExtra", "multtest", "zCompositions"]
},
"AMARETTO": {
"name": "AMARETTO",
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"sha256": "0n3w00x1qajkg43ip3l63k2qs0d1x2zv8wv4xj0iqwl6r6cqgxnf",
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},
"AMOUNTAIN": {
"name": "AMOUNTAIN",
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},
"ANCOMBC": {
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"depends": ["CVXR", "DescTools", "Hmisc", "MASS", "Matrix", "Rdpack", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "TreeSummarizedExperiment", "doParallel", "doRNG", "energy", "foreach", "gtools", "lme4", "lmerTest", "mia", "multcomp", "nloptr"]
},
"ANF": {
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"depends": ["Biobase", "MASS", "RColorBrewer", "igraph", "survival"]
},
"APAlyzer": {
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},
"APL": {
"name": "APL",
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"depends": ["Matrix", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "ggrepel", "magrittr", "org_Hs_eg_db", "org_Mm_eg_db", "plotly", "reticulate", "rlang", "topGO", "viridisLite"]
},
"ARRmNormalization": {
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"depends": ["ARRmData"]
},
"ASAFE": {
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},
"ASEB": {
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},
"ASGSCA": {
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"depends": ["MASS", "Matrix"]
},
"ASICS": {
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"depends": ["BiocParallel", "Matrix", "PepsNMR", "SummarizedExperiment", "ggplot2", "glmnet", "gridExtra", "mvtnorm", "plyr", "quadprog", "ropls", "zoo"]
},
"ASSET": {
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"sha256": "1wqsnp7w3ml7azrx72fafcfbmjg4324jaxcijpcrlrrccxl5rwp4",
"depends": ["MASS", "msm", "rmeta"]
},
"ASSIGN": {
"name": "ASSIGN",
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"sha256": "1aq302awy940jrc1hnsf0rn05y4fg5m9aljsl1mclxxig6b8mrd2",
"depends": ["Rlab", "ggplot2", "gplots", "msm", "sva", "yaml"]
},
"ASURAT": {
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"sha256": "1fjzmvc4if1kqhwzhd38l5ryvk2qg3001jwapbnkfagxkhmnwymg",
"depends": ["ComplexHeatmap", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "circlize", "cluster", "plot3D"]
},
"ASpli": {
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"sha256": "1br4apbc3zn06ilg8fjb8xcxaimz4h7rnx9i60ak4wnpvgzgbyh2",
"depends": ["AnnotationDbi", "BiocGenerics", "BiocStyle", "DT", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "MASS", "Rsamtools", "S4Vectors", "UpSetR", "data_table", "edgeR", "htmltools", "igraph", "limma", "pbmcapply", "tidyr", "txdbmaker"]
},
"ATACCoGAPS": {
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"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"]
},
"ATACseqQC": {
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},
"ATACseqTFEA": {
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},
"AUCell": {
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},
"AWFisher": {
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},
"AffyRNADegradation": {
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},
"AgiMicroRna": {
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"depends": ["Biobase", "affy", "affycoretools", "limma", "preprocessCore"]
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"AllelicImbalance": {
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},
"AlphaBeta": {
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},
"AlphaMissenseR": {
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"depends": ["BiocBaseUtils", "BiocFileCache", "DBI", "curl", "dplyr", "duckdb", "memoise", "rjsoncons", "rlang", "spdl", "whisker"]
},
"AlpsNMR": {
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},
"AnVIL": {
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},
"AnVILBilling": {
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},
"AnVILPublish": {
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},
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},
"AnnotationHub": {
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},
"AnnotationHubData": {
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},
"ArrayExpress": {
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"AssessORF": {
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"BADER": {
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"BAGS": {
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"depends": ["Biobase", "breastCancerVDX"]
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"BANDITS": {
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"depends": ["BiocParallel", "DRIMSeq", "MASS", "R_utils", "Rcpp", "RcppArmadillo", "data_table", "doParallel", "doRNG", "foreach", "ggplot2"]
},
"BASiCS": {
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"depends": ["Biobase", "BiocGenerics", "BiocParallel", "MASS", "Matrix", "Rcpp", "RcppArmadillo", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "assertthat", "coda", "cowplot", "ggExtra", "ggplot2", "hexbin", "matrixStats", "posterior", "reshape2", "scran", "scuttle", "viridis"]
},
"BASiCStan": {
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"depends": ["BASiCS", "BH", "Rcpp", "RcppEigen", "RcppParallel", "SingleCellExperiment", "StanHeaders", "SummarizedExperiment", "glmGamPoi", "rstan", "rstantools", "scran", "scuttle"]
},
"BBCAnalyzer": {
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"depends": ["Biostrings", "GenomicRanges", "IRanges", "Rsamtools", "SummarizedExperiment", "VariantAnnotation"]
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"BCRANK": {
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},
"BERT": {
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"depends": ["BiocParallel", "SummarizedExperiment", "cluster", "comprehenr", "foreach", "invgamma", "iterators", "janitor", "limma", "logging", "sva"]
},
"BEclear": {
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},
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}
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