{
  "_id": "6a32503d3efcd9bda437d9d8",
  "Package": "vissE",
  "Title": "Visualising Set Enrichment Analysis Results",
  "Version": "1.21.0",
  "Authors@R": "c(\nperson(given = \"Dharmesh D.\",\nfamily = \"Bhuva\",\nrole = c(\"aut\", \"cre\"),\nemail = \"bhuva.d@wehi.edu.au\",\ncomment = c(ORCID = \"0000-0002-6398-9157\")),\nperson(given = \"Ahmed\",\nfamily = \"Mohamed\",\nrole = c(\"ctb\"),\nemail = \"mohamed.a@wehi.edu.au\")\n)",
  "Description": "This package enables the interpretation and analysis of\nresults from a gene set enrichment analysis using network-based\nand text-mining approaches. Most enrichment analyses result in\nlarge lists of significant gene sets that are difficult to\ninterpret. Tools in this package help build a similarity-based\nnetwork of significant gene sets from a gene set enrichment\nanalysis that can then be investigated for their biological\nfunction using text-mining approaches.",
  "biocViews": "Software, GeneExpression, GeneSetEnrichment,\nNetworkEnrichment, Network",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyDataCompression": "bzip2",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.2.3",
  "URL": "https://davislaboratory.github.io/vissE",
  "BugReports": "https://github.com/DavisLaboratory/vissE/issues",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libfontconfig1-dev libfreetype6-dev libglpk-dev\nlibicu-dev libjpeg-dev libpng-dev libxml2-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:56:07 UTC",
  "RemoteUrl": "https://github.com/bioc/vissE",
  "RemoteRef": "HEAD",
  "RemoteSha": "faf767d8c4c9c3efdfe03a1dcfdd9c505a0add91",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-17 07:36:10 UTC",
    "User": "root"
  },
  "Author": "Dharmesh D. Bhuva [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-6398-9157>),\nAhmed Mohamed [ctb]",
  "Maintainer": "Dharmesh D. Bhuva <bhuva.d@wehi.edu.au>",
  "MD5sum": "e01cbb00b256e280215b16c3627a484c",
  "_user": "bioc",
  "_type": "src",
  "_file": "vissE_1.21.0.tar.gz",
  "_fileid": "d2d544a7dd3b8ce65324ffcaf62c7c784709fcf9f874063369b380cc3b6200b7",
  "_filesize": 515044,
  "_sha256": "d2d544a7dd3b8ce65324ffcaf62c7c784709fcf9f874063369b380cc3b6200b7",
  "_created": "2026-06-17T07:36:10.000Z",
  "_published": "2026-06-17T07:43:57.097Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 81842941529,
      "time": 282,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "FAILURE",
      "artifact": ""
    },
    {
      "job": 81842941539,
      "time": 300,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7688976633"
    },
    {
      "job": 81842941541,
      "time": 330,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7688988313"
    },
    {
      "job": 81842941545,
      "time": 150,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7688925717"
    },
    {
      "job": 81842941527,
      "time": 128,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7688923320"
    },
    {
      "job": 81841917026,
      "time": 394,
      "config": "source",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7688876792"
    },
    {
      "job": 81842941535,
      "time": 212,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7688948977"
    },
    {
      "job": 81842941665,
      "time": 256,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7688962271"
    },
    {
      "job": 81842941587,
      "time": 227,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7688952168"
    },
    {
      "job": 81842941601,
      "time": 245,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7688958549"
    }
  ],
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/27673099916",
  "_status": "failure",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/vissE",
  "_commit": {
    "id": "faf767d8c4c9c3efdfe03a1dcfdd9c505a0add91",
    "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": 1777380967
  },
  "_maintainer": {
    "name": "Dharmesh D. Bhuva",
    "email": "bhuva.d@wehi.edu.au",
    "orcid": "0000-0002-6398-9157"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1",
      "role": "Depends"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "scico",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "tm",
      "role": "Imports"
    },
    {
      "package": "ggwordcloud",
      "role": "Imports"
    },
    {
      "package": "GSEABase",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "ggforce",
      "role": "Imports"
    },
    {
      "package": "msigdb",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "textstem",
      "role": "Imports"
    },
    {
      "package": "tidygraph",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "ggraph",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Mm.eg.db",
      "role": "Suggests"
    },
    {
      "package": "patchwork",
      "role": "Suggests"
    },
    {
      "package": "singscore",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "prettydoc",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "pkgdown",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.21.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.20.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "geneexpression",
    "genesetenrichment",
    "networkenrichment",
    "network",
    "bioinformatics"
  ],
  "_stars": 19,
  "_contributors": [
    {
      "user": "bhuvad",
      "count": 10,
      "uuid": 30132854
    },
    {
      "user": "ahmohamed",
      "count": 9,
      "uuid": 6384340
    },
    {
      "user": "nturaga",
      "count": 6,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 6,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 440,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://github.com/davislaboratory/visse",
  "_pkgdown": "https://davislaboratory.github.io/vissE",
  "_searchresults": 25,
  "_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/readme.html",
    "extra/readme.md",
    "extra/vissE.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/davislaboratory/visse",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "bhuvad_theme",
    "characteriseGeneset",
    "computeMsigNetwork",
    "computeMsigOverlap",
    "computeMsigWordFreq",
    "findMsigClusters",
    "getMsigExclusionList",
    "plotGeneStats",
    "plotMsigNetwork",
    "plotMsigPPI",
    "plotMsigWordcloud"
  ],
  "_datasets": [
    {
      "name": "hgsc",
      "title": "The Hallmark collection from the MSigDB",
      "object": "hgsc",
      "file": "hgsc.rda",
      "class": [
        "GeneSetCollection"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "bhuvad_theme",
      "title": "Custom theme",
      "topics": [
        "bhuvad_theme"
      ]
    },
    {
      "page": "characteriseGeneset",
      "title": "Functionally characterise a list of genes",
      "topics": [
        "characteriseGeneset"
      ]
    },
    {
      "page": "computeMsigNetwork",
      "title": "Compute a network using computed gene set overlap",
      "topics": [
        "computeMsigNetwork"
      ]
    },
    {
      "page": "computeMsigOverlap",
      "title": "Compute gene set overlap",
      "topics": [
        "computeMsigOverlap"
      ]
    },
    {
      "page": "computeMsigWordFreq",
      "title": "Compute word frequencies for a single MSigDB collection",
      "topics": [
        "computeMsigWordFreq"
      ]
    },
    {
      "page": "findMsigClusters",
      "title": "Identify gene-set clusters from a gene-set overlap network",
      "topics": [
        "findMsigClusters"
      ]
    },
    {
      "page": "getMsigExclusionList",
      "title": "Exclusion list of words for MSigDB gene set text mining",
      "topics": [
        "getMsigExclusionList"
      ]
    },
    {
      "page": "hgsc",
      "title": "The Hallmark collection from the MSigDB",
      "topics": [
        "hgsc"
      ]
    },
    {
      "page": "plotGeneStats",
      "title": "Plot gene statistics for clusters of gene sets",
      "topics": [
        "plotGeneStats"
      ]
    },
    {
      "page": "plotMsigNetwork",
      "title": "Plot a gene set overlap network",
      "topics": [
        "plotMsigNetwork"
      ]
    },
    {
      "page": "plotMsigPPI",
      "title": "Plot PPI network for gene-set clusters identified using vissE",
      "topics": [
        "plotMsigPPI"
      ]
    },
    {
      "page": "plotMsigWordcloud",
      "title": "Compute and plot word frequencies for multiple MSigDB collections",
      "topics": [
        "plotMsigWordcloud"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/vissE/raw/HEAD/README.md",
  "_rundeps": [
    "annotate",
    "AnnotationDbi",
    "AnnotationHub",
    "askpass",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocManager",
    "BiocVersion",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "colorspace",
    "commonmark",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "digest",
    "dplyr",
    "dtt",
    "english",
    "ExperimentHub",
    "farver",
    "fastmap",
    "fastmatch",
    "filelock",
    "generics",
    "ggforce",
    "ggplot2",
    "ggraph",
    "ggrepel",
    "ggwordcloud",
    "glue",
    "graph",
    "graphlayouts",
    "gridExtra",
    "gridtext",
    "GSEABase",
    "gtable",
    "httr",
    "httr2",
    "hunspell",
    "igraph",
    "IRanges",
    "isoband",
    "ISOcodes",
    "jpeg",
    "jsonlite",
    "KEGGREST",
    "koRpus",
    "koRpus.lang.en",
    "labeling",
    "lattice",
    "lexicon",
    "lifecycle",
    "litedown",
    "magrittr",
    "markdown",
    "MASS",
    "Matrix",
    "memoise",
    "mgsub",
    "mime",
    "msigdb",
    "NLP",
    "openssl",
    "org.Hs.eg.db",
    "org.Mm.eg.db",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "polyclip",
    "purrr",
    "qdapRegex",
    "quanteda",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "reshape2",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "S7",
    "scales",
    "scico",
    "Seqinfo",
    "slam",
    "SnowballC",
    "stopwords",
    "stringi",
    "stringr",
    "sylly",
    "sylly.en",
    "sys",
    "systemfonts",
    "syuzhet",
    "textclean",
    "textshape",
    "textstem",
    "tibble",
    "tidygraph",
    "tidyr",
    "tidyselect",
    "tm",
    "tweenr",
    "utf8",
    "vctrs",
    "viridis",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "xtable",
    "XVector",
    "yaml",
    "zoo"
  ],
  "_score": 5.153814864344529,
  "_indexed": true,
  "_nocasepkg": "visse",
  "_universes": [
    "bioc",
    "davislaboratory"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.21.0",
      "date": "2026-06-17T07:42:01.000Z",
      "distro": "noble",
      "commit": "faf767d8c4c9c3efdfe03a1dcfdd9c505a0add91",
      "fileid": "391c37fddfad01d35d9a9acb191db784099251a2451241eef72631bf0169f064",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27673099916"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.21.0",
      "date": "2026-06-17T07:42:41.000Z",
      "distro": "noble",
      "commit": "faf767d8c4c9c3efdfe03a1dcfdd9c505a0add91",
      "fileid": "8fb39e7406a78a9af71749f33572f63271905ade04b8b07e3600b2d3836bd08d",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27673099916"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.21.0",
      "date": "2026-06-17T07:39:43.000Z",
      "commit": "faf767d8c4c9c3efdfe03a1dcfdd9c505a0add91",
      "fileid": "3c28216dd820778db626a01af3a021d8226d73a2425eabf09f4afea3cc25c693",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27673099916"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.21.0",
      "date": "2026-06-17T07:39:47.000Z",
      "commit": "faf767d8c4c9c3efdfe03a1dcfdd9c505a0add91",
      "fileid": "7dee10835ebe85c5dba3e9814a2b6fd3b9daf0a027e04f78b29c655c6e1da8b8",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27673099916"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.21.0",
      "date": "2026-06-17T07:41:39.000Z",
      "commit": "faf767d8c4c9c3efdfe03a1dcfdd9c505a0add91",
      "fileid": "b8df8018e60002cb390aa169e94798c3d96bfcc0aebdb1a85bbee7fe0ef92ee9",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27673099916"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.21.0",
      "date": "2026-06-17T07:41:11.000Z",
      "commit": "faf767d8c4c9c3efdfe03a1dcfdd9c505a0add91",
      "fileid": "5247ccc99df539fd55d3be866f0a091f02c65b90df3c6bdcbaf0cbd9ee7bbe7c",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27673099916"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.21.0",
      "date": "2026-06-17T07:40:41.000Z",
      "commit": "faf767d8c4c9c3efdfe03a1dcfdd9c505a0add91",
      "fileid": "9cbff5fac2ec75de3c1381123405a34fd4e69ccd43bb04b1fd12d74a4204fe3f",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27673099916"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.21.0",
      "date": "2026-06-17T07:41:02.000Z",
      "commit": "faf767d8c4c9c3efdfe03a1dcfdd9c505a0add91",
      "fileid": "62aa085c3cfa59c672f3fb9faa626958200fbd77d6b91fe85949008d1750fcbc",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27673099916"
    }
  ]
}