nixpkgs/pkgs/development/r-modules/bioc-packages.json

{
  "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",
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      "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",
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      "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",
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      "sha256": "0wx54jf44i6qy7q46dki7pjdkmddq9zvzjj1v0s2izhr73xgrrfw",
      "depends": ["ComplexHeatmap", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "circlize", "cluster", "plot3D"]
    },
    "ASpli": {
      "name": "ASpli",
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      "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",
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      "sha256": "0wksn7l5g5k6cm3y1c4gsjrc37zf73w6nbzcdqb3p93lmnyk2dh2",
      "depends": ["BiocGenerics", "DelayedArray", "DelayedMatrixStats", "GSEABase", "Matrix", "R_utils", "SummarizedExperiment", "data_table", "mixtools"]
    },
    "AWFisher": {
      "name": "AWFisher",
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      "depends": ["edgeR", "limma"]
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    "AffiXcan": {
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      "depends": ["BiocParallel", "MultiAssayExperiment", "SummarizedExperiment", "crayon"]
    },
    "AffyRNADegradation": {
      "name": "AffyRNADegradation",
      "version": "1.54.0",
      "sha256": "1sq5mawmykd14vvw6854mdpdc8qqn52l3z131by79j1sklbjah0d",
      "depends": ["affy"]
    },
    "AgiMicroRna": {
      "name": "AgiMicroRna",
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      "sha256": "1fqslyiwl3d9i2qvvhispf5g340vsl7wd2z61lfjw43p0azjlr1m",
      "depends": ["Biobase", "affy", "affycoretools", "limma", "preprocessCore"]
    },
    "AllelicImbalance": {
      "name": "AllelicImbalance",
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      "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",
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      "depends": ["BiocParallel", "data_table", "dplyr", "expm", "ggplot2", "gtools", "igraph", "optimx", "plotly", "stringr"]
    },
    "AlphaMissenseR": {
      "name": "AlphaMissenseR",
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      "sha256": "0zxdq9afill3dkfvc0ykdr3vxz568siigxdb30n9va8kdf34iqwm",
      "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": {
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    },
    "AnVILAz": {
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    },
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    },
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      "name": "Anaquin",
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      "sha256": "09f1pfy06jzhwbxjvh126yxnahk3y6hmcy5793wxnpgsy6wmmabl",
      "depends": ["DESeq2", "ROCR", "ggplot2", "knitr", "locfit", "plyr", "qvalue"]
    },
    "AneuFinder": {
      "name": "AneuFinder",
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      "depends": ["AneuFinderData", "BiocGenerics", "Biostrings", "DNAcopy", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "bamsignals", "cowplot", "doParallel", "ecp", "foreach", "ggdendro", "ggplot2", "ggrepel", "mclust", "reshape2"]
    },
    "AnnotationDbi": {
      "name": "AnnotationDbi",
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      "depends": ["Biobase", "BiocGenerics", "DBI", "IRanges", "KEGGREST", "RSQLite", "S4Vectors"]
    },
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      "depends": ["GenomicRanges", "lazyeval"]
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      "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "DBI", "RCurl", "RSQLite", "S4Vectors", "XML"]
    },
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      "depends": ["AnnotationDbi", "BiocFileCache", "BiocGenerics", "BiocManager", "BiocVersion", "RSQLite", "S4Vectors", "curl", "dplyr", "httr", "rappdirs", "yaml"]
    },
    "AnnotationHubData": {
      "name": "AnnotationHubData",
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      "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",
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      "sha256": "0wiaczf6qvi5qaidjp7hlfh5d054dswalgwrf9a4xd6407nx6nj5",
      "depends": ["Biobase", "httr", "jsonlite", "limma", "oligo", "rlang"]
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    "AssessORF": {
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      "depends": ["Biobase", "breastCancerVDX"]
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      "depends": ["BiocParallel", "DRIMSeq", "MASS", "R_utils", "Rcpp", "RcppArmadillo", "data_table", "doParallel", "doRNG", "foreach", "ggplot2"]
    },
    "BASiCS": {
      "name": "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": {
      "name": "BASiCStan",
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      "depends": ["BASiCS", "BH", "Rcpp", "RcppEigen", "RcppParallel", "SingleCellExperiment", "StanHeaders", "SummarizedExperiment", "glmGamPoi", "rstan", "rstantools", "scran", "scuttle"]
    },
    "BBCAnalyzer": {
      "name": "BBCAnalyzer",
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      "depends": ["Biostrings", "GenomicRanges", "IRanges", "Rsamtools", "SummarizedExperiment", "VariantAnnotation"]
    },
    "BCRANK": {
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