{
  "_id": "6ae75bb31e2c7b3a4f53024f",
  "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": "2026-11-01 13:25:15 UTC",
    "User": "root"
  },
  "Author": "Monther Alhamdoosh [aut, cre],\nLuyi Tian [aut],\nMilica Ng [aut],\nMatthew Ritchie [ctb]",
  "Maintainer": "Monther Alhamdoosh <m.hamdoosh@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "EGSEA_1.41.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/0197e281d681354c6bd65a179df7d2b569342e4d7986b97271a7b8517051e072",
  "_filesize": 2370875,
  "_sha256": "0197e281d681354c6bd65a179df7d2b569342e4d7986b97271a7b8517051e072",
  "_expires": "2027-02-09T15:33:05.000Z",
  "_created": "2026-11-01T13:25:15.000Z",
  "_published": "2026-11-01T15:33:07.472Z",
  "_upstream": "https://github.com/bioc/EGSEA",
  "_status": "success",
  "_maintainer": {
    "name": "Monther Alhamdoosh",
    "email": "m.hamdoosh@gmail.com",
    "login": "malhamdoosh",
    "linkedin": "in/malhamdoosh",
    "description": "This is the official account of Dr Monther Alhamdoosh's R&D Lab. ",
    "uuid": 6373094
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  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
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    "geneexpression",
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    "genetics",
    "microarray",
    "multiplecomparison",
    "onechannel",
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    "systemsbiology",
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    "type": "organization",
    "name": "Bioconductor",
    "followers": 482,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_downloads": {
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    "source": "https://www.bioconductor.org/packages/stats/bioc/EGSEA"
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  "_searchresults": 90,
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        "key": "EGSEA::EGSEAResults",
        "hash": "f8b425eb5fec138c"
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      {
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        "key": "EGSEA::generic:addSymbolsMap",
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    "extra/citation.html",
    "extra/citation.json",
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    "extra/contents.json",
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    "extra/manual.pdf",
    "extra/NEWS.html",
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    "extra/readme.html",
    "extra/readme.md"
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  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
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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
    }
  ],
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      "page": "EGSEA-package",
      "title": "Ensemble of Gene Enrichment Analysis (EGSEA)",
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        "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",
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        "buildKEGGIdx,egsea-index",
        "buildMSigDBIdx",
        "buildMSigDBIdx,egsea-index"
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    },
    {
      "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"
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    {
      "page": "egsea-aux",
      "title": "EGSEA auxiliary functions",
      "topics": [
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        "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",
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    "SparseArray",
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    "sparseMatrixStats",
    "SpatialExperiment",
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    "SummarizedExperiment",
    "survival",
    "sys",
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    "TH.data",
    "tibble",
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    "utf8",
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  "_vignettes": [
    {
      "source": "EGSEA.Rnw",
      "filename": "EGSEA.pdf",
      "title": "EGSEA vignette",
      "engine": "knitr::knitr",
      "headings": [
        "1 Introduction",
        "2 Citation",
        "3 Installation instructions",
        "4 Quick start",
        "5 S4 classes and methods",
        "6 Ensemble of Gene Set Enrichment Analysis",
        "7 EGSEA report",
        "8 EGSEA on a non-human dataset",
        "9 EGSEA on a count matrix",
        "10 EGSEA on a list of genes",
        "11 Non-standard gene set collections",
        "12 Adding new GSE method",
        "13 Packages used",
        "References"
      ],
      "created": "2016-04-18 21:59:28",
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