{
  "_id": "6a1ae8601d7bb097a09f2006",
  "Package": "ReactomePA",
  "Type": "Package",
  "Title": "Reactome Pathway Analysis",
  "Version": "1.57.0",
  "Authors@R": "c(person(given = \"Guangchuang\", family = \"Yu\",\nemail = \"guangchuangyu@gmail.com\",\nrole  = c(\"aut\", \"cre\")),\nperson(given = \"Vladislav\", family = \"Petyuk\",\nemail = \"petyuk@gmail.com\",\nrole  = \"ctb\"))",
  "Maintainer": "Guangchuang Yu <guangchuangyu@gmail.com>",
  "Description": "This package provides functions for pathway analysis based\non REACTOME pathway database. It implements enrichment\nanalysis, gene set enrichment analysis and several functions\nfor visualization. This package is not affiliated with the\nReactome team.",
  "VignetteBuilder": "knitr",
  "ByteCompile": "true",
  "License": "GPL-2",
  "URL": "https://yulab-smu.top/contribution-knowledge-mining/",
  "BugReports": "https://github.com/GuangchuangYu/ReactomePA/issues",
  "Packaged": {
    "Date": "2026-05-30 09:37:22 UTC",
    "User": "root"
  },
  "biocViews": "Pathways, Visualization, Annotation, MultipleComparison,\nGeneSetEnrichment, Reactome",
  "RoxygenNote": "7.3.3",
  "Encoding": "UTF-8",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:36:22 UTC",
  "RemoteUrl": "https://github.com/bioc/ReactomePA",
  "RemoteRef": "HEAD",
  "RemoteSha": "d04e108b02a83c8504acd198478f54b303b20cc6",
  "NeedsCompilation": "no",
  "Author": "Guangchuang Yu [aut, cre],\nVladislav Petyuk [ctb]",
  "MD5sum": "2eb05bbae310a175982d12bd4222aec9",
  "_user": "bioc",
  "_type": "src",
  "_file": "ReactomePA_1.57.0.tar.gz",
  "_fileid": "554bcc6662cff2682a8f335f32145e1e82f95caa1a54bbfbfda110962110eff6",
  "_filesize": 116385,
  "_sha256": "554bcc6662cff2682a8f335f32145e1e82f95caa1a54bbfbfda110962110eff6",
  "_created": "2026-05-30T09:37:22.000Z",
  "_published": "2026-05-30T13:38:40.300Z",
  "_jobs": [
    {
      "job": 78640126469,
      "time": 263,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7307345147"
    },
    {
      "job": 78640126479,
      "time": 418,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7307359819"
    },
    {
      "job": 78640126474,
      "time": 539,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307370656"
    },
    {
      "job": 78640126475,
      "time": 208,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7308568301"
    },
    {
      "job": 78640126513,
      "time": 246,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7308573848"
    },
    {
      "job": 78639426139,
      "time": 322,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307231961"
    },
    {
      "job": 78640126463,
      "time": 224,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307341291"
    },
    {
      "job": 78640126523,
      "time": 747,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7307391429"
    },
    {
      "job": 78640126484,
      "time": 552,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7307373518"
    },
    {
      "job": 78640126489,
      "time": 299,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307350148"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 2,
    "note": 11
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26675855279",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/ReactomePA",
  "_commit": {
    "id": "d04e108b02a83c8504acd198478f54b303b20cc6",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777379782
  },
  "_maintainer": {
    "name": "Guangchuang Yu",
    "email": "guangchuangyu@gmail.com",
    "login": "guangchuangyu",
    "twitter": "@guangchuangyu",
    "description": "Professor of Bioinformatics at Southern Medical University.",
    "uuid": 626539
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4.0",
      "role": "Depends"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "enrichplot",
      "role": "Imports"
    },
    {
      "package": "enrichit",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.3.5",
      "role": "Imports"
    },
    {
      "package": "ggraph",
      "role": "Imports"
    },
    {
      "package": "reactome.db",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "graphite",
      "role": "Imports"
    },
    {
      "package": "gson",
      "role": "Imports"
    },
    {
      "package": "yulab.utils",
      "version": ">= 0.1.5",
      "role": "Imports"
    },
    {
      "package": "clusterProfiler",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    },
    {
      "package": "prettydoc",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 9,
  "_updates": [
    {
      "week": "2025-44",
      "n": 1
    },
    {
      "week": "2025-49",
      "n": 1
    },
    {
      "week": "2025-52",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.57.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.56.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "pathways",
    "visualization",
    "annotation",
    "multiplecomparison",
    "genesetenrichment",
    "reactome",
    "enrichment-analysis",
    "reactome-pathway-analysis",
    "reactomepa"
  ],
  "_stars": 45,
  "_contributors": [
    {
      "user": "guangchuangyu",
      "count": 218,
      "uuid": 626539
    },
    {
      "user": "dtenenba",
      "count": 24,
      "uuid": 2286826
    },
    {
      "user": "jwokaty",
      "count": 16,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "vladpetyuk",
      "count": 8,
      "uuid": 4207635
    },
    {
      "user": "nelson-gon",
      "count": 5,
      "uuid": 42792514
    },
    {
      "user": "huerqiang",
      "count": 5,
      "uuid": 48857018
    },
    {
      "user": "clearmind777",
      "count": 2,
      "uuid": 139222736
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "sonali-bioc",
      "count": 2,
      "uuid": 6373953
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 5828,
    "source": "https://www.bioconductor.org/packages/stats/bioc/ReactomePA"
  },
  "_mentions": 171,
  "_devurl": "https://github.com/guangchuangyu/reactomepa",
  "_searchresults": 2128,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/ReactomePA.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/yulab-smu/reactomepa",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "cnetplot",
    "dotplot",
    "emapplot",
    "enrichPathway",
    "geneID",
    "geneInCategory",
    "gseaplot",
    "gsePathway",
    "gson_Reactome",
    "heatplot",
    "ridgeplot",
    "viewPathway"
  ],
  "_help": [
    {
      "page": "DataSet",
      "title": "Datasets sample contains a sample of gene IDs.",
      "topics": [
        "DataSet"
      ]
    },
    {
      "page": "enrichPathway",
      "title": "Pathway Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enriched pathways with FDR control.",
      "topics": [
        "enrichPathway"
      ]
    },
    {
      "page": "getALLEG",
      "title": "getALLEG",
      "topics": [
        "getALLEG"
      ]
    },
    {
      "page": "getDb",
      "title": "getDb",
      "topics": [
        "getDb"
      ]
    },
    {
      "page": "gsePathway",
      "title": "gsePathway",
      "topics": [
        "gsePathway"
      ]
    },
    {
      "page": "gson_Reactome",
      "title": "gson_Reactome",
      "topics": [
        "gson_Reactome"
      ]
    },
    {
      "page": "viewPathway",
      "title": "viewPathway",
      "topics": [
        "viewPathway"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/ReactomePA/raw/HEAD/README.md",
  "_rundeps": [
    "AnnotationDbi",
    "ape",
    "aplot",
    "askpass",
    "base64enc",
    "Biobase",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "bslib",
    "cachem",
    "cli",
    "cluster",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "digest",
    "dir.expiry",
    "DOSE",
    "dplyr",
    "enrichit",
    "enrichplot",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "fontBitstreamVera",
    "fontLiberation",
    "fontquiver",
    "fs",
    "gdtools",
    "generics",
    "ggforce",
    "ggfun",
    "ggiraph",
    "ggnewscale",
    "ggplot2",
    "ggplotify",
    "ggraph",
    "ggrepel",
    "ggtangle",
    "ggtree",
    "glue",
    "GO.db",
    "GOSemSim",
    "graph",
    "graphite",
    "graphlayouts",
    "gridExtra",
    "gridGraphics",
    "gson",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr",
    "igraph",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "memoise",
    "mime",
    "nlme",
    "openssl",
    "patchwork",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "polyclip",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "reactome.db",
    "reshape2",
    "rlang",
    "rmarkdown",
    "RSQLite",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "scatterpie",
    "Seqinfo",
    "stringi",
    "stringr",
    "sys",
    "systemfonts",
    "tibble",
    "tidydr",
    "tidygraph",
    "tidyr",
    "tidyselect",
    "tidytree",
    "tinytex",
    "treeio",
    "tweenr",
    "utf8",
    "vctrs",
    "viridis",
    "viridisLite",
    "withr",
    "xfun",
    "XVector",
    "yaml",
    "yulab.utils"
  ],
  "_vignettes": [
    {
      "source": "ReactomePA.Rmd",
      "filename": "ReactomePA.html",
      "title": "An R package for Reactome Pathway Analysis",
      "author": "Guangchuang Yu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Vignette",
        "Citation",
        "Need help?"
      ],
      "created": "2015-06-29 08:08:51",
      "modified": "2025-12-07 03:28:41",
      "commits": 26
    }
  ],
  "_score": 12.479097440319276,
  "_indexed": true,
  "_nocasepkg": "reactomepa",
  "_universes": [
    "bioc",
    "guangchuangyu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.57.0",
      "date": "2026-05-30T09:57:06.000Z",
      "distro": "noble",
      "commit": "d04e108b02a83c8504acd198478f54b303b20cc6",
      "fileid": "6ac58e610cead4fa181a6ebef3de093033f2df65744c625bbe7028bc2de8d2c5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675855279"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.57.0",
      "date": "2026-05-30T09:59:04.000Z",
      "distro": "noble",
      "commit": "d04e108b02a83c8504acd198478f54b303b20cc6",
      "fileid": "6e6c07dee33333ad54e99a96be63fd779c01530dc476311289d1005249cbf4a4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675855279"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.57.0",
      "date": "2026-05-30T13:36:01.000Z",
      "commit": "d04e108b02a83c8504acd198478f54b303b20cc6",
      "fileid": "925be50ae1fa3e65eb1aa72c76e14809bfd80d549320c399536081e643b6dfba",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675855279"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.57.0",
      "date": "2026-05-30T13:36:11.000Z",
      "commit": "d04e108b02a83c8504acd198478f54b303b20cc6",
      "fileid": "40bf48df652354e8fcd5778e06eb5343952e496230dac445c4347e94ced540a2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675855279"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.57.0",
      "date": "2026-05-30T09:56:10.000Z",
      "commit": "d04e108b02a83c8504acd198478f54b303b20cc6",
      "fileid": "f6119fc1845e19e162709430b3292eed1503bf0863f38a5f83dc290c831be1f6",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675855279"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.57.0",
      "date": "2026-05-30T10:01:39.000Z",
      "commit": "d04e108b02a83c8504acd198478f54b303b20cc6",
      "fileid": "a66a33c56165f9ac5a075dec3254e7ab34b29b52d6c3e16fd9748a1a826a4173",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675855279"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.57.0",
      "date": "2026-05-30T09:59:45.000Z",
      "commit": "d04e108b02a83c8504acd198478f54b303b20cc6",
      "fileid": "bacae1cf4b5e7c25438aba0be4f5daaef71856aa9cf1c4c57ce72407e4f38ac6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675855279"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.57.0",
      "date": "2026-05-30T09:55:08.000Z",
      "commit": "d04e108b02a83c8504acd198478f54b303b20cc6",
      "fileid": "da685ef1d9093f4c7c94ac8d135acb23a4d2ebcadd5d2689af0b758c045055f7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675855279"
    }
  ]
}