{
  "_id": "6a1add111d7bb097a09eab16",
  "Package": "hypeR",
  "Title": "An R Package For Geneset Enrichment Workflows",
  "Version": "2.10.0",
  "Authors@R": "c(person(given=\"Anthony\", family=\"Federico\", email=\"anfed@bu.edu\", \nrole=c(\"aut\")),\nperson(given=\"Andrew\", family=\"Chen\", email=\"andrewdr@bu.edu\",\nrole=c(\"aut\", \"cre\")),\nperson(given=\"Stefano\", family=\"Monti\", email=\"smonti@bu.edu\",\nrole=c(\"aut\")))",
  "Description": "An R Package for Geneset Enrichment Workflows.",
  "License": "GPL-3 + file LICENSE",
  "URL": "https://github.com/montilab/hypeR",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.1",
  "biocViews": "GeneSetEnrichment, Annotation, Pathways",
  "VignetteBuilder": "knitr",
  "BugReports": "https://github.com/montilab/hypeR/issues",
  "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev libglpk-dev make libharfbuzz-dev libicu-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 13:06:00 UTC",
  "RemoteUrl": "https://github.com/bioc/hypeR",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "6ec1e801bf5f79814c280cceb6a229596caed183",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:12:25 UTC",
    "User": "root"
  },
  "Author": "Anthony Federico [aut],\nAndrew Chen [aut, cre],\nStefano Monti [aut]",
  "Maintainer": "Andrew Chen <andrewdr@bu.edu>",
  "MD5sum": "c183d4a6bc2d90fd6b3ddb2bd0caa21a",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "hypeR_2.10.0.tar.gz",
  "_fileid": "92de77ef0ae3ae8037e95f51203a9d33152c093d4781d951d103ac557e4a2064",
  "_filesize": 254865,
  "_sha256": "92de77ef0ae3ae8037e95f51203a9d33152c093d4781d951d103ac557e4a2064",
  "_created": "2026-05-30T09:12:25.000Z",
  "_published": "2026-05-30T12:50:25.977Z",
  "_jobs": [
    {
      "job": 78638873985,
      "time": 180,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7307126395"
    },
    {
      "job": 78638873983,
      "time": 408,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307147627"
    },
    {
      "job": 78638873989,
      "time": 387,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307145680"
    },
    {
      "job": 78638873981,
      "time": 205,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7308302292"
    },
    {
      "job": 78638873987,
      "time": 280,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7308228378"
    },
    {
      "job": 78638635046,
      "time": 236,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307089113"
    },
    {
      "job": 78638873980,
      "time": 156,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307124079"
    },
    {
      "job": 78638873986,
      "time": 714,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307176934"
    },
    {
      "job": 78638874005,
      "time": 672,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7307172951"
    },
    {
      "job": 78638873999,
      "time": 310,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307139059"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 2,
    "note": 14
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621611909",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/hypeR",
  "_commit": {
    "id": "6ec1e801bf5f79814c280cceb6a229596caed183",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777381560
  },
  "_maintainer": {
    "name": "Andrew Chen",
    "email": "andrewdr@bu.edu",
    "login": "andrewdchen",
    "description": "Bioinformatics @ BU",
    "uuid": 31497311
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggforce",
      "role": "Imports"
    },
    {
      "package": "R6",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "httr",
      "role": "Imports"
    },
    {
      "package": "openxlsx",
      "role": "Imports"
    },
    {
      "package": "htmltools",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "reactable",
      "role": "Imports"
    },
    {
      "package": "msigdbr",
      "role": "Imports"
    },
    {
      "package": "kableExtra",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "visNetwork",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Imports"
    },
    {
      "package": "tidyverse",
      "role": "Suggests"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-23",
      "n": 4
    },
    {
      "week": "2025-33",
      "n": 1
    },
    {
      "week": "2025-47",
      "n": 1
    },
    {
      "week": "2025-49",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.11.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.10.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "genesetenrichment",
    "annotation",
    "pathways",
    "bioinformatics",
    "computational-biology",
    "geneset-enrichment-analysis"
  ],
  "_stars": 79,
  "_contributors": [
    {
      "user": "anfederico",
      "count": 225,
      "uuid": 18452646
    },
    {
      "user": "nturaga",
      "count": 15,
      "uuid": 2746443
    },
    {
      "user": "tetomonti",
      "count": 15,
      "uuid": 9437983
    },
    {
      "user": "andrewdchen",
      "count": 13,
      "uuid": 31497311
    },
    {
      "user": "jwokaty",
      "count": 13,
      "uuid": 1744257
    },
    {
      "user": "lshep",
      "count": 3,
      "uuid": 18724380
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 440,
    "source": "https://www.bioconductor.org/packages/stats/bioc/hypeR"
  },
  "_mentions": 3,
  "_devurl": "https://github.com/montilab/hyper",
  "_searchresults": 176,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/hypeR.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/montilab/hyper",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "clean_genesets",
    "enrichr_available",
    "enrichr_download",
    "enrichr_gsets",
    "genesets_Server",
    "genesets_UI",
    "ggempty",
    "ggeplot",
    "ggvenn",
    "gsets",
    "hyp",
    "hyp_dots",
    "hyp_emap",
    "hyp_hmap",
    "hyp_show",
    "hyp_to_excel",
    "hyp_to_graph",
    "hyp_to_rmd",
    "hyp_to_table",
    "hypeR",
    "hyperdb_available",
    "hyperdb_gsets",
    "hyperdb_rgsets",
    "msigdb_available",
    "msigdb_download",
    "msigdb_gsets",
    "msigdb_info",
    "msigdb_species",
    "msigdb_version",
    "multihyp",
    "rctbl_build",
    "rctbl_hyp",
    "rctbl_mhyp",
    "rgsets"
  ],
  "_help": [
    {
      "page": "clean_genesets",
      "title": "Clean labels of genesets",
      "topics": [
        "clean_genesets"
      ]
    },
    {
      "page": "enrichr_available",
      "title": "Get enrichr available genesets",
      "topics": [
        "enrichr_available"
      ]
    },
    {
      "page": "enrichr_download",
      "title": "Download data from enrichr in the form of a named list",
      "topics": [
        "enrichr_download"
      ]
    },
    {
      "page": "enrichr_gsets",
      "title": "Download data from enrichr in the form of a gsets object",
      "topics": [
        "enrichr_gsets"
      ]
    },
    {
      "page": "genesets_Server",
      "title": "Shiny server module for geneset selection",
      "topics": [
        "genesets_Server"
      ]
    },
    {
      "page": "genesets_UI",
      "title": "Shiny interface module for geneset selection",
      "topics": [
        "genesets_UI"
      ]
    },
    {
      "page": "ggempty",
      "title": "An empty ggplot",
      "topics": [
        "ggempty"
      ]
    },
    {
      "page": "ggeplot",
      "title": "Enrichment plot implemented in ggplot",
      "topics": [
        "ggeplot"
      ]
    },
    {
      "page": "ggvenn",
      "title": "Venn diagram implemented in ggplot",
      "topics": [
        "ggvenn"
      ]
    },
    {
      "page": "gsets",
      "title": "A genesets object",
      "topics": [
        "gsets"
      ]
    },
    {
      "page": "hyp",
      "title": "A hyp object",
      "topics": [
        "hyp"
      ]
    },
    {
      "page": "hyp_dots",
      "title": "Visualize hyp/multihyp objects as a dots plot",
      "topics": [
        "hyp_dots"
      ]
    },
    {
      "page": "hyp_emap",
      "title": "Visualize hyp/multihyp objects as an enrichment map",
      "topics": [
        "hyp_emap"
      ]
    },
    {
      "page": "hyp_hmap",
      "title": "Visualize hyp/multihyp objects as a hiearchy map",
      "topics": [
        "hyp_hmap"
      ]
    },
    {
      "page": "hyp_show",
      "title": "Convert a hyp object to a reactable table",
      "topics": [
        "hyp_show"
      ]
    },
    {
      "page": "hyp_to_excel",
      "title": "Export hyp/multihyp object to excel",
      "topics": [
        "hyp_to_excel"
      ]
    },
    {
      "page": "hyp_to_graph",
      "title": "Convert a hyp object to an igraph object",
      "topics": [
        "hyp_to_graph"
      ]
    },
    {
      "page": "hyp_to_rmd",
      "title": "Export hyp object to rmarkdown",
      "topics": [
        "hyp_to_rmd"
      ]
    },
    {
      "page": "hyp_to_table",
      "title": "Export hyp/multihyp object to table",
      "topics": [
        "hyp_to_table"
      ]
    },
    {
      "page": "hypeR",
      "title": "Calculate enrichment of one or more signatures",
      "topics": [
        "hypeR"
      ]
    },
    {
      "page": "hyperdb_available",
      "title": "Check available data to download from hyperdb",
      "topics": [
        "hyperdb_available"
      ]
    },
    {
      "page": "hyperdb_gsets",
      "title": "Download data from hyperdb",
      "topics": [
        "hyperdb_gsets"
      ]
    },
    {
      "page": "hyperdb_rgsets",
      "title": "Download data from hyperdb in the form of a rgsets object",
      "topics": [
        "hyperdb_rgsets"
      ]
    },
    {
      "page": "limma",
      "title": "Differential Expression",
      "topics": [
        "limma"
      ]
    },
    {
      "page": "msigdb_available",
      "title": "Get msigdbr available genesets",
      "topics": [
        "msigdb_available"
      ]
    },
    {
      "page": "msigdb_download",
      "title": "Download data from msigdb in the form of a named list",
      "topics": [
        "msigdb_download"
      ]
    },
    {
      "page": "msigdb_gsets",
      "title": "Download data from msigdb in the form of a gsets object",
      "topics": [
        "msigdb_gsets"
      ]
    },
    {
      "page": "msigdb_info",
      "title": "Print msigdb gsets information",
      "topics": [
        "msigdb_info"
      ]
    },
    {
      "page": "msigdb_species",
      "title": "Get msigdbr available species",
      "topics": [
        "msigdb_species"
      ]
    },
    {
      "page": "msigdb_version",
      "title": "Get msigdbr package version number",
      "topics": [
        "msigdb_version"
      ]
    },
    {
      "page": "multihyp",
      "title": "A multihyp object",
      "topics": [
        "multihyp"
      ]
    },
    {
      "page": "rctbl_build",
      "title": "Reactable builder for hyp or mhyp objects",
      "topics": [
        "rctbl_build"
      ]
    },
    {
      "page": "rctbl_hyp",
      "title": "Reactable table for hyp objects",
      "topics": [
        "rctbl_hyp"
      ]
    },
    {
      "page": "rctbl_mhyp",
      "title": "Reactable table for multihyp objects",
      "topics": [
        "rctbl_mhyp"
      ]
    },
    {
      "page": "rgsets",
      "title": "A relational genesets object",
      "topics": [
        "rgsets"
      ]
    },
    {
      "page": "wgcna",
      "title": "Co-expression Modules",
      "topics": [
        "wgcna"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/hypeR/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "askpass",
    "assertthat",
    "babelgene",
    "base64enc",
    "BiocManager",
    "BiocStyle",
    "bookdown",
    "bslib",
    "cachem",
    "cli",
    "commonmark",
    "cpp11",
    "curl",
    "digest",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "generics",
    "ggforce",
    "ggplot2",
    "glue",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "igraph",
    "isoband",
    "jquerylib",
    "jsonlite",
    "kableExtra",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "memoise",
    "mime",
    "msigdbr",
    "openssl",
    "openxlsx",
    "otel",
    "pillar",
    "pkgconfig",
    "plyr",
    "polyclip",
    "promises",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "reactable",
    "reactR",
    "reshape2",
    "rlang",
    "rmarkdown",
    "rstudioapi",
    "S7",
    "sass",
    "scales",
    "shiny",
    "sourcetools",
    "stringi",
    "stringr",
    "svglite",
    "sys",
    "systemfonts",
    "textshaping",
    "tibble",
    "tidyselect",
    "tinytex",
    "tweenr",
    "utf8",
    "vctrs",
    "viridisLite",
    "visNetwork",
    "withr",
    "xfun",
    "xml2",
    "xtable",
    "yaml",
    "zip"
  ],
  "_vignettes": [
    {
      "source": "hypeR.Rmd",
      "filename": "hypeR.html",
      "title": "hypeR",
      "author": "Anthony Federico, Stefano Monti",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Documentation",
        "Requirements",
        "Installation",
        "Usage",
        "Signature",
        "Geneset",
        "Downloading Genesets",
        "Enrichment",
        "Reproducibility",
        "Downstream Methods"
      ],
      "created": "2019-01-29 19:30:23",
      "modified": "2025-06-02 22:35:38",
      "commits": 22
    }
  ],
  "_score": 8.717171026832311,
  "_indexed": false,
  "_nocasepkg": "hyper",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/hypeR",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.10.0",
      "date": "2026-05-30T09:19:32.000Z",
      "distro": "noble",
      "commit": "6ec1e801bf5f79814c280cceb6a229596caed183",
      "fileid": "d98dbd383e633d3a3ae50b65a543d4b20c00dcb85ff2abde6ed7ee4642d50c7c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621611909"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.10.0",
      "date": "2026-05-30T09:19:06.000Z",
      "distro": "noble",
      "commit": "6ec1e801bf5f79814c280cceb6a229596caed183",
      "fileid": "b33292d867c5e12115c11f70795469ade5ca63c06bca9669ddfa15beba0c308d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621611909"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.10.0",
      "date": "2026-05-30T12:47:56.000Z",
      "commit": "6ec1e801bf5f79814c280cceb6a229596caed183",
      "fileid": "895e048fad5e76296879663603ba0ab0a165b4e65e4f28f713d6d69448b80a28",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621611909"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.10.0",
      "date": "2026-05-30T12:35:45.000Z",
      "commit": "6ec1e801bf5f79814c280cceb6a229596caed183",
      "fileid": "a20772c1c1859e35c64118227ad1b206bee38d1324b1f84f6a0702fe925028bc",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621611909"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.10.0",
      "date": "2026-05-30T09:18:52.000Z",
      "commit": "6ec1e801bf5f79814c280cceb6a229596caed183",
      "fileid": "3c5e470f7a3583498fcc5aebadb58192f0e9fc656df30b2cdbf061f8718770d8",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621611909"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.10.0",
      "date": "2026-05-30T09:23:55.000Z",
      "commit": "6ec1e801bf5f79814c280cceb6a229596caed183",
      "fileid": "d0cc7f94dc4b25f8a062242b6ae7d8310fb3e8f9c0d8ff68023a11dd2d4de69e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621611909"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.10.0",
      "date": "2026-05-30T09:23:28.000Z",
      "commit": "6ec1e801bf5f79814c280cceb6a229596caed183",
      "fileid": "1609f1dddf03aeb1b57c908b53b1470041fabbaab38e76db066add21b9c02d3e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621611909"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.10.0",
      "date": "2026-05-30T09:17:21.000Z",
      "commit": "6ec1e801bf5f79814c280cceb6a229596caed183",
      "fileid": "38fc861311f30e9b43a0ec5c5c2799f16746e7f2dd4f787c13c00c5dc11ebe04",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621611909"
    }
  ]
}