{
  "_id": "6a1e97201d7bb097a0a6cc7b",
  "Package": "GSEAmining",
  "Type": "Package",
  "Title": "Make Biological Sense of Gene Set Enrichment Analysis Outputs",
  "Version": "1.23.0",
  "Authors@R": "person(\"Oriol\", \"Arqués\", email = \"oriol.arques@gmail.com\",\nrole = c(\"aut\", \"cre\"))",
  "Description": "Gene Set Enrichment Analysis is a very powerful and\ninteresting computational method that allows an easy\ncorrelation between differential expressed genes and biological\nprocesses. Unfortunately, although it was designed to help\nresearchers to interpret gene expression data it can generate\nhuge amounts of results whose biological meaning can be\ndifficult to interpret. Many available tools rely on the\nhierarchically structured Gene Ontology (GO) classification to\nreduce reundandcy in the results. However, due to the\npopularity of GSEA many more gene set collections, such as\nthose in the Molecular Signatures Database are emerging. Since\nthese collections are not organized as those in GO, their usage\nfor GSEA do not always give a straightforward answer or, in\nother words, getting all the meaninful information can be\nchallenging with the currently available tools. For these\nreasons, GSEAmining was born to be an easy tool to create\nreproducible reports to help researchers make biological sense\nof GSEA outputs. Given the results of GSEA, GSEAmining clusters\nthe different gene sets collections based on the presence of\nthe same genes in the leadind edge (core) subset. Leading edge\nsubsets are those genes that contribute most to the enrichment\nscore of each collection of genes or gene sets. For this\nreason, gene sets that participate in similar biological\nprocesses should share genes in common and in turn cluster\ntogether. After that, GSEAmining is able to identify and\nrepresent for each cluster: - The most enriched terms in the\nnames of gene sets (as wordclouds) - The most enriched genes in\nthe leading edge subsets (as bar plots). In each case, positive\nand negative enrichments are shown in different colors so it is\neasy to distinguish biological processes or genes that may be\nof interest in that particular study.",
  "License": "GPL-3 | file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.1.0",
  "VignetteBuilder": "knitr",
  "biocViews": "GeneSetEnrichment, Clustering, Visualization",
  "Config/pak/sysreqs": "libicu-dev libjpeg-dev libpng-dev libxml2-dev\nlibssl-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:53:08 UTC",
  "RemoteUrl": "https://github.com/bioc/GSEAmining",
  "RemoteRef": "HEAD",
  "RemoteSha": "7b07dc9e9e9d3c558be2348b7fe6a2e541e94f1a",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-02 08:35:11 UTC",
    "User": "root"
  },
  "Author": "Oriol Arqu��s [aut, cre]",
  "Maintainer": "Oriol Arqués <oriol.arques@gmail.com>",
  "MD5sum": "b06ad6e1a744e9f2204dfe98ee27d4a8",
  "_user": "bioc",
  "_type": "src",
  "_file": "GSEAmining_1.23.0.tar.gz",
  "_fileid": "a3bd59d730ddfecac154e7d7a68d433be2121f5967a93f7ab70231f34270867d",
  "_filesize": 2866628,
  "_sha256": "a3bd59d730ddfecac154e7d7a68d433be2121f5967a93f7ab70231f34270867d",
  "_created": "2026-06-02T08:35:11.000Z",
  "_published": "2026-06-02T08:41:04.945Z",
  "_jobs": [
    {
      "job": 79031486382,
      "time": 193,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7352907946"
    },
    {
      "job": 79031486394,
      "time": 252,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7352928135"
    },
    {
      "job": 79031486442,
      "time": 311,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7352947929"
    },
    {
      "job": 79031486411,
      "time": 118,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7352899870"
    },
    {
      "job": 79031486455,
      "time": 108,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7352912316"
    },
    {
      "job": 79030505299,
      "time": 340,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7352839544"
    },
    {
      "job": 79031486425,
      "time": 169,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7352899668"
    },
    {
      "job": 79031486399,
      "time": 168,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7352899598"
    },
    {
      "job": 79031486427,
      "time": 204,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7352914438"
    },
    {
      "job": 79031486580,
      "time": 151,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7352893731"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26808028200",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/GSEAmining",
  "_commit": {
    "id": "7b07dc9e9e9d3c558be2348b7fe6a2e541e94f1a",
    "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": 1777380788
  },
  "_maintainer": {
    "name": "Oriol Arqués",
    "email": "oriol.arques@gmail.com",
    "login": "oriolarques",
    "description": "",
    "uuid": 32706992
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "tidytext",
      "role": "Imports"
    },
    {
      "package": "dendextend",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggwordcloud",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "clusterProfiler",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "tm",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.23.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.22.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "genesetenrichment",
    "clustering",
    "visualization"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 342,
    "source": "https://www.bioconductor.org/packages/stats/bioc/GSEAmining"
  },
  "_searchresults": 7,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/GSEAmining.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "clust_group_cores",
    "clust_group_terms",
    "clust_groups",
    "gm_clust",
    "gm_dendplot",
    "gm_enrichcores",
    "gm_enrichreport",
    "gm_enrichterms",
    "gm_filter",
    "stop_words"
  ],
  "_datasets": [
    {
      "name": "genesets_sel",
      "title": "Selected gene sets as test",
      "object": "genesets_sel",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "NES",
        "p.adjust",
        "core_enrichment"
      ],
      "rows": 52,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "clust_group_cores",
      "title": "clust_group_cores",
      "topics": [
        "clust_group_cores"
      ]
    },
    {
      "page": "clust_group_terms",
      "title": "clust_group_terms",
      "topics": [
        "clust_group_terms"
      ]
    },
    {
      "page": "clust_groups",
      "title": "clust_groups",
      "topics": [
        "clust_groups"
      ]
    },
    {
      "page": "genesets_sel",
      "title": "Selected gene sets as test",
      "topics": [
        "genesets_sel"
      ]
    },
    {
      "page": "gm_clust",
      "title": "gm_clust: GSEAmining cluster object",
      "topics": [
        "gm_clust"
      ]
    },
    {
      "page": "gm_dendplot",
      "title": "gm_dendplot: GSEAmining dendrogram plotter",
      "topics": [
        "gm_dendplot"
      ]
    },
    {
      "page": "gm_enrichcores",
      "title": "gm_enrichcores: GSEAmining core enrichment genes",
      "topics": [
        "gm_enrichcores"
      ]
    },
    {
      "page": "gm_enrichreport",
      "title": "gm_enrichreport: GSEAmining Enrichment Report",
      "topics": [
        "gm_enrichreport"
      ]
    },
    {
      "page": "gm_enrichterms",
      "title": "gm_enrichterms: GSEAmining enriched terms",
      "topics": [
        "gm_enrichterms"
      ]
    },
    {
      "page": "gm_filter",
      "title": "gm_filter: GSEAmining GSEA output filter",
      "topics": [
        "gm_filter"
      ]
    },
    {
      "page": "stop_words",
      "title": "Stop words. Eliminates the first word of the gene sets from MSigDb that relate to the origin of the gene set. Additionally it eliminates words that do not add a lot of significance such as prepositions or adverbs among others.",
      "topics": [
        "stop_words"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/GSEAmining/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "colorspace",
    "commonmark",
    "cpp11",
    "curl",
    "dendextend",
    "dplyr",
    "farver",
    "generics",
    "ggplot2",
    "ggwordcloud",
    "glue",
    "gridExtra",
    "gridtext",
    "gtable",
    "isoband",
    "janeaustenr",
    "jpeg",
    "labeling",
    "lattice",
    "lifecycle",
    "litedown",
    "magrittr",
    "markdown",
    "Matrix",
    "pillar",
    "pkgconfig",
    "png",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "S7",
    "scales",
    "SnowballC",
    "stringi",
    "stringr",
    "tibble",
    "tidyselect",
    "tidytext",
    "tokenizers",
    "utf8",
    "vctrs",
    "viridis",
    "viridisLite",
    "withr",
    "xfun",
    "xml2"
  ],
  "_vignettes": [
    {
      "source": "GSEAmining.Rmd",
      "filename": "GSEAmining.html",
      "title": "GSEAmining",
      "author": "Oriol Arqués",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Installation",
        "Input data format: gm_filter",
        "Clustering",
        "gm_clust: Creation of a gm_clust object",
        "gm_dendplot: Plot the cluster",
        "Evaluation of gene sets enriched terms by cluster",
        "Evaluation of gene enrichment in leading edge subsets by clusters",
        "gm_enrichreport: Create a report",
        "SessionInfo()"
      ],
      "created": "2020-06-12 10:19:12",
      "modified": "2020-06-12 10:19:12",
      "commits": 1
    }
  ],
  "_score": 4,
  "_indexed": true,
  "_nocasepkg": "gseamining",
  "_universes": [
    "bioc",
    "oriolarques"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-06-02T08:38:49.000Z",
      "distro": "noble",
      "commit": "7b07dc9e9e9d3c558be2348b7fe6a2e541e94f1a",
      "fileid": "864b1236380cbf248f5b60c0519f12ed11a23ce42d86d1fe4e3db32b963a3b37",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808028200"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-06-02T08:39:49.000Z",
      "distro": "noble",
      "commit": "7b07dc9e9e9d3c558be2348b7fe6a2e541e94f1a",
      "fileid": "ad5c21f1e7be501cdc44b67b6d841a09ed36c71dee03614be782a12a9419e0b1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808028200"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-06-02T08:37:56.000Z",
      "commit": "7b07dc9e9e9d3c558be2348b7fe6a2e541e94f1a",
      "fileid": "ee26d59c79c7ee6f82ea21fd7422c0b3b083d8d1cf164b57df1eaac577b2f5ce",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808028200"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-06-02T08:38:29.000Z",
      "commit": "7b07dc9e9e9d3c558be2348b7fe6a2e541e94f1a",
      "fileid": "2e38b16b11a2b24d0422608e22e0a1b3117c288c11bcb520d5b31c5700c2a800",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808028200"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.23.0",
      "date": "2026-06-02T08:38:26.000Z",
      "commit": "7b07dc9e9e9d3c558be2348b7fe6a2e541e94f1a",
      "fileid": "13bcf14556766585bac955fbaf19aee6ce77f3c86b2c2ab18e25fe42b7d150bf",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808028200"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-06-02T08:37:20.000Z",
      "commit": "7b07dc9e9e9d3c558be2348b7fe6a2e541e94f1a",
      "fileid": "7571b89c5f1c6431e47b302d67f1b80d52fa81ff410bc7661418f29d5523c614",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808028200"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-06-02T08:38:01.000Z",
      "commit": "7b07dc9e9e9d3c558be2348b7fe6a2e541e94f1a",
      "fileid": "b8af109c5d25cf8ea91611d054670dede007b782a54a470121f5113b93587845",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808028200"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-06-02T08:37:05.000Z",
      "commit": "7b07dc9e9e9d3c558be2348b7fe6a2e541e94f1a",
      "fileid": "f26f0dc2965a14ca2e713b1a4f6192c20fe6c5d37f622e5438ab9e5ea5812c54",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808028200"
    }
  ]
}