{
  "_id": "6a1afcfd1d7bb097a09fdbf0",
  "Package": "EGSEA",
  "Title": "Ensemble of Gene Set Enrichment Analyses",
  "Version": "1.41.0",
  "Authors@R": "c(person(given=\"Monther\", family=\"Alhamdoosh\", role=c(\"aut\", \"cre\"),\nemail=\"m.hamdoosh@gmail.com\"),\nperson(given=\"Luyi\", family=\"Tian\", role=c(\"aut\")),\nperson(given=\"Milica\", family=\"Ng\", role=c(\"aut\")),\nperson(\"Matthew\", \"Ritchie\",role=c(\"ctb\"),\nemail=\"mritchie@wehi.edu.au\"))",
  "Description": "This package implements the Ensemble of Gene Set\nEnrichment Analyses (EGSEA) method for gene set testing. EGSEA\nalgorithm utilizes the analysis results of twelve prominent GSE\nalgorithms in the literature to calculate collective\nsignificance scores for each gene set.",
  "biocViews": "ImmunoOncology, DifferentialExpression, GO, GeneExpression,\nGeneSetEnrichment, Genetics, Microarray, MultipleComparison,\nOneChannel, Pathways, RNASeq, Sequencing, Software,\nSystemsBiology, TwoChannel,Metabolomics, Proteomics, KEGG,\nGraphAndNetwork, GeneSignaling, GeneTarget, NetworkEnrichment,\nNetwork, Classification",
  "License": "GPL-3",
  "LazyLoad": "yes",
  "NeedsCompilation": "no",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.2.3",
  "Config/pak/sysreqs": "cmake libfftw3-dev make libmagick++-dev gsfonts\nlibicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:43:30 UTC",
  "RemoteUrl": "https://github.com/bioc/EGSEA",
  "RemoteRef": "HEAD",
  "RemoteSha": "c0c96af231848598863e0dded4809ffb1e6f06ae",
  "Packaged": {
    "Date": "2026-05-30 09:50:52 UTC",
    "User": "root"
  },
  "Author": "Monther Alhamdoosh [aut, cre],\nLuyi Tian [aut],\nMilica Ng [aut],\nMatthew Ritchie [ctb]",
  "Maintainer": "Monther Alhamdoosh <m.hamdoosh@gmail.com>",
  "MD5sum": "4ff6b6c8cbe2fe0537d3003952fc31d6",
  "_user": "bioc",
  "_type": "src",
  "_file": "EGSEA_1.41.0.tar.gz",
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  "_filesize": 2377111,
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  "_created": "2026-05-30T09:50:52.000Z",
  "_published": "2026-05-30T15:06:37.107Z",
  "_jobs": [
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      "job": 78640842546,
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    "warning": 1,
    "note": 15
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676526488",
  "_status": "success",
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  "_upstream": "https://github.com/bioc/EGSEA",
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    "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",
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    "name": "Monther Alhamdoosh",
    "email": "m.hamdoosh@gmail.com",
    "login": "malhamdoosh",
    "description": "Leading bioinformatics in the pharma industry.",
    "uuid": 6373094
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    },
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      "package": "DT",
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    },
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      "package": "BiocStyle",
      "role": "Suggests"
    },
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      "package": "knitr",
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  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
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  ],
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    "differentialexpression",
    "go",
    "geneexpression",
    "genesetenrichment",
    "genetics",
    "microarray",
    "multiplecomparison",
    "onechannel",
    "pathways",
    "rnaseq",
    "sequencing",
    "software",
    "systemsbiology",
    "twochannel",
    "metabolomics",
    "proteomics",
    "kegg",
    "graphandnetwork",
    "genesignaling",
    "genetarget",
    "networkenrichment",
    "network",
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    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
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    "source": "https://www.bioconductor.org/packages/stats/bioc/EGSEA"
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  "_searchresults": 71,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/EGSEA.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
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    "buildGeneSetDBIdx",
    "buildGMTIdx",
    "buildIdx",
    "buildKEGGIdx",
    "buildMSigDBIdx",
    "egsea",
    "egsea.base",
    "egsea.cnt",
    "egsea.combine",
    "egsea.logo",
    "egsea.ma",
    "egsea.ora",
    "egsea.sort",
    "generateReport",
    "getlimmaResults",
    "getSetByID",
    "getSetByName",
    "getSetScores",
    "limmaTopTable",
    "plotBars",
    "plotGOGraph",
    "plotHeatmap",
    "plotMethods",
    "plotPathway",
    "plotSummary",
    "plotSummaryHeatmap",
    "show",
    "showSetByID",
    "showSetByName",
    "topSets"
  ],
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      "name": "arraydata",
      "title": "Example dataset for 'egsea.ma'",
      "object": "arraydata",
      "file": "arraydata.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "EGSEA-package",
      "title": "Ensemble of Gene Enrichment Analysis (EGSEA)",
      "topics": [
        "EGSEA-package",
        "EGSEA"
      ]
    },
    {
      "page": "arraydata",
      "title": "Example dataset for 'egsea.ma'",
      "topics": [
        "arraydata"
      ]
    },
    {
      "page": "egsea-index",
      "title": "Functions to create gene set collection indexes for EGSEA",
      "topics": [
        "buildCustomIdx",
        "buildCustomIdx,egsea-index",
        "buildGeneSetDBIdx",
        "buildGeneSetDBIdx,egsea-index",
        "buildGMTIdx",
        "buildGMTIdx,egsea-index",
        "buildIdx",
        "buildIdx,egsea-index",
        "buildKEGGIdx",
        "buildKEGGIdx,egsea-index",
        "buildMSigDBIdx",
        "buildMSigDBIdx,egsea-index"
      ]
    },
    {
      "page": "egsea-main",
      "title": "Core functions to perform ensemble of gene set enrichment analysis (EGSEA)",
      "topics": [
        "egsea",
        "egsea,egsea-main",
        "egsea.cnt",
        "egsea.cnt,egsea-main",
        "egsea.ma",
        "egsea.ora",
        "egsea.ora,egsea-main"
      ]
    },
    {
      "page": "egsea-aux",
      "title": "EGSEA auxiliary functions",
      "topics": [
        "egsea.base",
        "egsea.base,egsea-aux",
        "egsea.combine",
        "egsea.combine,egsea-aux",
        "egsea.logo",
        "egsea.logo,egsea-aux",
        "egsea.sort",
        "egsea.sort,egsea-aux"
      ]
    },
    {
      "page": "EGSEAResults-methods",
      "title": "The EGSEAResults class",
      "topics": [
        "$,EGSEAResults-method",
        "EGSEAResults",
        "EGSEAResults-class",
        "generateReport",
        "generateReport,EGSEAResults-method",
        "getlimmaResults",
        "getlimmaResults,EGSEAResults-method",
        "getSetScores",
        "getSetScores,EGSEAResults-method",
        "limmaTopTable",
        "limmaTopTable,EGSEAResults-method",
        "plotBars",
        "plotBars,EGSEAResults-method",
        "plotGOGraph",
        "plotGOGraph,EGSEAResults-method",
        "plotHeatmap",
        "plotHeatmap,EGSEAResults-method",
        "plotMethods",
        "plotMethods,EGSEAResults-method",
        "plotPathway",
        "plotPathway,EGSEAResults-method",
        "plotSummary",
        "plotSummary,EGSEAResults-method",
        "plotSummaryHeatmap",
        "plotSummaryHeatmap,EGSEAResults-method",
        "show,EGSEAResults-method",
        "showSetByID",
        "showSetByID,EGSEAResults-method",
        "showSetByName",
        "showSetByName,EGSEAResults-method",
        "summary,EGSEAResults-method",
        "topSets",
        "topSets,EGSEAResults-method"
      ]
    },
    {
      "page": "GSCollectionIndex-methods",
      "title": "The GSCollectionIndex class",
      "topics": [
        "$,GSCollectionIndex-method",
        "getSetByID",
        "getSetByID,GSCollectionIndex-method",
        "getSetByName",
        "getSetByName,GSCollectionIndex-method",
        "GSCollectionIndex",
        "GSCollectionIndex-class",
        "show,GSCollectionIndex-method",
        "summary,GSCollectionIndex-method"
      ]
    }
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      "title": "EGSEA vignette",
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      "headings": [],
      "created": "2016-04-18 21:59:28",
      "modified": "2018-07-25 05:49:42",
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