nixpkgs/pkgs/development/r-modules/bioc-packages.json
2024-08-19 12:01:54 +10:00

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JSON

{
"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",
"version": "1.14.0",
"sha256": "0kihg0mwm2ysgnx3jg6xln7ibvgmky0x2hjbcmdqlg65znczh4b6",
"depends": ["BiocParallel", "DrImpute", "MASS", "Matrix", "S4Vectors", "SAVER", "SingleCellExperiment", "SummarizedExperiment", "checkmate", "data_table", "kernlab", "rsvd"]
},
"ADaCGH2": {
"name": "ADaCGH2",
"version": "2.44.0",
"sha256": "1j9dn0xw8mdfvi2ccm1d5j9q740wb89wqi6715n6jy3dljlc8irz",
"depends": ["DNAcopy", "GLAD", "aCGH", "bit", "cluster", "ff", "tilingArray", "waveslim"]
},
"AGDEX": {
"name": "AGDEX",
"version": "1.52.0",
"sha256": "088r2ahqjv61wnzp7by4c5v9aivahmyfkzr7prnkk3ff8zh6pznl",
"depends": ["Biobase", "GSEABase"]
},
"AHMassBank": {
"name": "AHMassBank",
"version": "1.4.0",
"sha256": "1inlsknrkb5am3aqfp3mk1fd0aaj89wfiq1549k7dqy71ng7rpf9",
"depends": ["AnnotationHubData"]
},
"AIMS": {
"name": "AIMS",
"version": "1.36.0",
"sha256": "0ljdv1gww01yi0h9j9br8kp67k5wizr1dy0091kngjcbn0dxzmla",
"depends": ["Biobase", "e1071"]
},
"ALDEx2": {
"name": "ALDEx2",
"version": "1.36.0",
"sha256": "1bqpk93bbyajw2dm54d68f3dkc0jgcny109asfm6kcz7dg7szi3y",
"depends": ["BiocParallel", "GenomicRanges", "IRanges", "Rfast", "S4Vectors", "SummarizedExperiment", "directlabels", "lattice", "latticeExtra", "multtest", "zCompositions"]
},
"AMARETTO": {
"name": "AMARETTO",
"version": "1.20.0",
"sha256": "0n3w00x1qajkg43ip3l63k2qs0d1x2zv8wv4xj0iqwl6r6cqgxnf",
"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": "1.30.0",
"sha256": "1y2k1vg31siic6j98700m54sswbj6wr4dvbw2mz3hlm0nmsmpxc1",
"depends": []
},
"ANCOMBC": {
"name": "ANCOMBC",
"version": "2.6.0",
"sha256": "14jdfcv3hghl1z2f7zj2mdqdyblz5sn4l1iwh8bhvih86cpigb58",
"depends": ["CVXR", "DescTools", "Hmisc", "MASS", "Matrix", "Rdpack", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "TreeSummarizedExperiment", "doParallel", "doRNG", "energy", "foreach", "gtools", "lme4", "lmerTest", "mia", "multcomp", "nloptr"]
},
"ANF": {
"name": "ANF",
"version": "1.26.0",
"sha256": "00s2rlkh5snqmvlz5a21ilmm0ngh4g362y7iayr6f78nh8gwp617",
"depends": ["Biobase", "MASS", "RColorBrewer", "igraph", "survival"]
},
"APAlyzer": {
"name": "APAlyzer",
"version": "1.18.0",
"sha256": "102zs1rlz58dzvrgidf7cvq4wcmk6sffc9fv4b0xlqk5d6il32w4",
"depends": ["DESeq2", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "HybridMTest", "Rsamtools", "Rsubread", "SummarizedExperiment", "VariantAnnotation", "dplyr", "ggplot2", "ggrepel", "repmis", "rtracklayer", "tidyr"]
},
"APL": {
"name": "APL",
"version": "1.8.0",
"sha256": "1mkm9aad0qamqs7595mqcbz37qz4ykn0y24wsl3ngj6ifyfxf643",
"depends": ["Matrix", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "ggrepel", "magrittr", "org_Hs_eg_db", "org_Mm_eg_db", "plotly", "reticulate", "rlang", "topGO", "viridisLite"]
},
"ARRmNormalization": {
"name": "ARRmNormalization",
"version": "1.44.0",
"sha256": "0wg799c5pzw9g0dbkaa5j4jyccvixqbc8x3xnwk3cgi1dsbhpk34",
"depends": ["ARRmData"]
},
"ASAFE": {
"name": "ASAFE",
"version": "1.30.0",
"sha256": "13qf4jvf0m6i46bwqxdhd4zllac370ckwnd9xh6p56r1lrgcl4sa",
"depends": []
},
"ASEB": {
"name": "ASEB",
"version": "1.48.0",
"sha256": "1h5rgy2n7rxd72ypzwnfclw8h5hvdnac48fgbfll669z2k97dsmm",
"depends": []
},
"ASGSCA": {
"name": "ASGSCA",
"version": "1.38.0",
"sha256": "0gvpb1pspm7zlllg77fbi3g6csa3cpp2lbljna2m0xfi0c5zdqvw",
"depends": ["MASS", "Matrix"]
},
"ASICS": {
"name": "ASICS",
"version": "2.20.1",
"sha256": "0halznbl3bflnn38rh9h5a5f0dsc88n6x6kwdffbpnin9i192q1k",
"depends": ["BiocParallel", "Matrix", "PepsNMR", "SummarizedExperiment", "ggplot2", "glmnet", "gridExtra", "mvtnorm", "plyr", "quadprog", "ropls", "zoo"]
},
"ASSET": {
"name": "ASSET",
"version": "2.22.0",
"sha256": "1wqsnp7w3ml7azrx72fafcfbmjg4324jaxcijpcrlrrccxl5rwp4",
"depends": ["MASS", "msm", "rmeta"]
},
"ASSIGN": {
"name": "ASSIGN",
"version": "1.40.0",
"sha256": "1aq302awy940jrc1hnsf0rn05y4fg5m9aljsl1mclxxig6b8mrd2",
"depends": ["Rlab", "ggplot2", "gplots", "msm", "sva", "yaml"]
},
"ASURAT": {
"name": "ASURAT",
"version": "1.8.0",
"sha256": "1fjzmvc4if1kqhwzhd38l5ryvk2qg3001jwapbnkfagxkhmnwymg",
"depends": ["ComplexHeatmap", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "circlize", "cluster", "plot3D"]
},
"ASpli": {
"name": "ASpli",
"version": "2.14.0",
"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": {
"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"]
},
"ATACseqQC": {
"name": "ATACseqQC",
"version": "1.28.0",
"sha256": "0licdpzhh6xlma0hnvs4rr4bjr5q4q3g18kipf0is47zj4l91smy",
"depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "ChIPpeakAnno", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "GenomicScores", "IRanges", "KernSmooth", "Rsamtools", "S4Vectors", "edgeR", "limma", "motifStack", "preseqR", "randomForest", "rtracklayer"]
},
"ATACseqTFEA": {
"name": "ATACseqTFEA",
"version": "1.6.0",
"sha256": "1dfw6vb0fx02xx21msvy8iarwmn41p1l3ryx1zs39668bz6zz06j",
"depends": ["BiocGenerics", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Matrix", "Rsamtools", "S4Vectors", "SummarizedExperiment", "TFBSTools", "dplyr", "ggplot2", "ggrepel", "limma", "motifmatchr", "pracma", "rtracklayer"]
},
"AUCell": {
"name": "AUCell",
"version": "1.26.0",
"sha256": "009ha82393giapvmfw2mi8pmi88f61mr69qj64y5vphcr1smvcl0",
"depends": ["BiocGenerics", "DelayedArray", "DelayedMatrixStats", "GSEABase", "Matrix", "R_utils", "SummarizedExperiment", "data_table", "mixtools"]
},
"AWFisher": {
"name": "AWFisher",
"version": "1.18.0",
"sha256": "0z5qs337zqqri2g3m69m85xg4x5sxnqlkbwz83vhnqfzmy9nqym0",
"depends": ["edgeR", "limma"]
},
"AffiXcan": {
"name": "AffiXcan",
"version": "1.22.0",
"sha256": "1241vpqkv4p3yarr6fsz1a7awvc4ff7q75ia3ra7vgkvg7gx9p93",
"depends": ["BiocParallel", "MultiAssayExperiment", "SummarizedExperiment", "crayon"]
},
"AffyRNADegradation": {
"name": "AffyRNADegradation",
"version": "1.50.0",
"sha256": "19lcs76jsdy5dz57rkdb8qqankpasrw2r5z4cy98q94az6582ix4",
"depends": ["affy"]
},
"AgiMicroRna": {
"name": "AgiMicroRna",
"version": "2.54.0",
"sha256": "1bm8rxfdgd0fx48fi70by08qr855jv6r4xcr7al2v9akv6vphws2",
"depends": ["Biobase", "affy", "affycoretools", "limma", "preprocessCore"]
},
"AllelicImbalance": {
"name": "AllelicImbalance",
"version": "1.42.0",
"sha256": "0mbmw450gdlr46ggvhrgimkbir3lg5dnqsfadn7yyrn7wkcr302f",
"depends": ["AnnotationDbi", "BSgenome", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "gridExtra", "lattice", "latticeExtra", "nlme", "seqinr"]
},
"AlphaBeta": {
"name": "AlphaBeta",
"version": "1.18.0",
"sha256": "192jyfw2676x8pgcp9h4d78283p7n6gnsdw7wzphfjn12v266fb5",
"depends": ["BiocParallel", "data_table", "dplyr", "expm", "ggplot2", "gtools", "igraph", "optimx", "plotly", "stringr"]
},
"AlphaMissenseR": {
"name": "AlphaMissenseR",
"version": "1.0.2",
"sha256": "1y8dzcrjqmqagnl4jiwcsfkj28n544j2d6li0ga6rrqmjwrnxzv0",
"depends": ["BiocBaseUtils", "BiocFileCache", "DBI", "curl", "dplyr", "duckdb", "memoise", "rjsoncons", "rlang", "spdl", "whisker"]
},
"AlpsNMR": {
"name": "AlpsNMR",
"version": "4.6.0",
"sha256": "1c8ynw9424ygc4wj4drbm9gdkdqwgb5z7p72zk3x5zh3zqai0d1d",
"depends": ["BiocParallel", "baseline", "cli", "dplyr", "fs", "future", "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": "1.16.1",
"sha256": "0i4skg2bpj0rbb3fbaprfs4d4nxg9aj8d6pni4a3k0wip3dw1cf9",
"depends": ["BiocBaseUtils", "BiocManager", "DT", "dplyr", "futile_logger", "htmltools", "httr", "jsonlite", "miniUI", "rapiclient", "rlang", "shiny", "tibble", "tidyr", "tidyselect", "yaml"]
},
"AnVILBilling": {
"name": "AnVILBilling",
"version": "1.14.0",
"sha256": "0z05zp70l7r1wxf1s825gsgaj6kzj4fgw3962gp0z90whz398jyf",
"depends": ["DBI", "DT", "bigrquery", "dplyr", "ggplot2", "lubridate", "magrittr", "plotly", "shiny", "shinytoastr"]
},
"AnVILPublish": {
"name": "AnVILPublish",
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"sha256": "030bm9hxqzgfp94h64wfizcbp4q8b9h2irk4zv679v0wnbspp3zz",
"depends": ["AnVIL", "BiocBaseUtils", "BiocManager", "httr", "jsonlite", "readr", "rmarkdown", "whisker", "yaml"]
},
"AnVILWorkflow": {
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"depends": ["AnVIL", "dplyr", "httr", "jsonlite", "tibble"]
},
"Anaquin": {
"name": "Anaquin",
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"sha256": "0hfvwzkfy6bm2ffghax5b228k2l6wf8zq82q13h6bxfps4wz0jgb",
"depends": ["DESeq2", "ROCR", "ggplot2", "knitr", "locfit", "plyr", "qvalue"]
},
"AneuFinder": {
"name": "AneuFinder",
"version": "1.32.0",
"sha256": "0dgmg0slyrh025wgz299dzzmpirlmdhmabxspci1qfarakw5yicf",
"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": "1.66.0",
"sha256": "1g2yzbx7djkk8kccbclxv953iijmjvsjsalfv1ihmmcai33979rs",
"depends": ["Biobase", "BiocGenerics", "DBI", "IRanges", "KEGGREST", "RSQLite", "S4Vectors"]
},
"AnnotationFilter": {
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"depends": ["GenomicRanges", "lazyeval"]
},
"AnnotationForge": {
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"depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "DBI", "RCurl", "RSQLite", "S4Vectors", "XML"]
},
"AnnotationHub": {
"name": "AnnotationHub",
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"sha256": "1da2n13j2xysnd175zi7s6zm8yllnp0k59vygkx9id85jcldqf51",
"depends": ["AnnotationDbi", "BiocFileCache", "BiocGenerics", "BiocManager", "BiocVersion", "RSQLite", "S4Vectors", "curl", "dplyr", "httr", "rappdirs", "yaml"]
},
"AnnotationHubData": {
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"sha256": "0wcbghjvgr8sx1qg9kyjxb7znkxhihy7jvzycrv4pyq746154xbi",
"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": "1.64.0",
"sha256": "1ad6h0pi04r9m3nwxrn7sha837m95kwii8z6s7j4zbka9ijy2pr4",
"depends": ["Biobase", "httr", "jsonlite", "limma", "oligo", "rlang"]
},
"AssessORF": {
"name": "AssessORF",
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"sha256": "1gzaafsfqzy2x35i251gvkd1syif80qb08kkvgnf1i6c8d2czmps",
"depends": ["Biostrings", "DECIPHER", "GenomicRanges", "IRanges"]
},
"BADER": {
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"sha256": "15lsvfmp4qsrv12bcrz5q8yz8xyg9rckrcflr3k6si03z2vw812p",
"depends": []
},
"BAGS": {
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"version": "2.44.0",
"sha256": "1xc7gp5fljqz26lj8sjcilm01g636p4wlzy4pzy5wgqxgfcw3zps",
"depends": ["Biobase", "breastCancerVDX"]
},
"BANDITS": {
"name": "BANDITS",
"version": "1.20.0",
"sha256": "1iizs0bvs7rbkwv3vs6xk26jy222kql80fp6cki0qs9h9igpzk5h",
"depends": ["BiocParallel", "DRIMSeq", "MASS", "R_utils", "Rcpp", "RcppArmadillo", "data_table", "doParallel", "doRNG", "foreach", "ggplot2"]
},
"BASiCS": {
"name": "BASiCS",
"version": "2.16.0",
"sha256": "0rcc8na0nravf2687bcvbaklwa0z8b43lvdy0nf9xvfrfpr1zjnw",
"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": "1.6.0",
"sha256": "1q6lhmdy19v30aq9hzphxicq6blyzr6z94wcqsqzwb0xjij1z5f9",
"depends": ["BASiCS", "BH", "Rcpp", "RcppEigen", "RcppParallel", "SingleCellExperiment", "StanHeaders", "SummarizedExperiment", "glmGamPoi", "rstan", "rstantools", "scran", "scuttle"]
},
"BBCAnalyzer": {
"name": "BBCAnalyzer",
"version": "1.34.0",
"sha256": "16zm6fix5f5277dkdaxyxl1q1n52960ma3vw8001a5bjxhic58rn",
"depends": ["Biostrings", "GenomicRanges", "IRanges", "Rsamtools", "SummarizedExperiment", "VariantAnnotation"]
},
"BCRANK": {
"name": "BCRANK",
"version": "1.66.0",
"sha256": "0ydajrbggvqakdf01pq5mqi1v3slz00irpbx4s9fmxvci9ganwp7",
"depends": ["Biostrings"]
},
"BEARscc": {
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"depends": ["SingleCellExperiment", "data_table", "ggplot2"]
},
"BEAT": {
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"sha256": "0s63nwf21ai1gys0dzjsjqy64sal7dpp040f0jqskyf2y6gdf9v9",
"depends": ["BSgenome", "Biostrings", "GenomicRanges", "ShortRead"]
},
"BERT": {
"name": "BERT",
"version": "1.0.0",
"sha256": "1n2v8sdvh40sqz8gpzszwhp2w6npxnl48bsp9l0bzz8w148cwyk8",
"depends": ["BiocParallel", "SummarizedExperiment", "cluster", "comprehenr", "foreach", "invgamma", "iterators", "janitor", "limma", "logging", "sva"]
},
"BEclear": {
"name": "BEclear",
"version": "2.20.0",
"sha256": "17i93h0q1fwl8wymmlgjsh8hbnaws6baf4jid5k579aap32zb5ha",
"depends": ["BiocParallel", "Matrix", "Rcpp", "Rdpack", "abind", "data_table", "dixonTest", "futile_logger", "ids"]
},
"BG2": {
"name": "BG2",
"version": "1.4.0",
"sha256": "0nby9b7kha4bz2x7a8b9nk78qai98m76csndnaikcpg79mpzygv5",
"depends": ["GA", "MASS", "Matrix", "caret", "memoise"]
},
"BHC": {
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