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  "Title": "Gene set enrichment data structures and methods",
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  "Description": "This package provides classes and methods to support Gene\nSet Enrichment Analysis (GSEA).",
  "License": "Artistic-2.0",
  "LazyLoad": "yes",
  "Collate": "utilities.R AAA.R AllClasses.R AllGenerics.R getObjects.R\nmethods-CollectionType.R methods-ExpressionSet.R\nmethods-GeneColorSet.R methods-GeneIdentifierType.R\nmethods-GeneSet.R methods-GeneSetCollection.R\nmethods-OBOCollection.R",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:32:25 UTC",
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    "toBroadXML",
    "toGmt",
    "union",
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    "updateObject",
    "urls",
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      "title": "Gene set enrichment data structures and methods",
      "topics": [
        "GSEABase-package",
        "GSEABase"
      ]
    },
    {
      "page": "CollectionType-constructors",
      "title": "Collection Type Class Constructors",
      "topics": [
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        "ChrCollection",
        "ChrlocCollection",
        "CollectionType",
        "ComputedCollection",
        "ExpressionSetCollection",
        "GOCollection",
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        "|,CollectionType,CollectionType-method"
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    },
    {
      "page": "details-methods",
      "title": "Methods for Displaying Detailed GeneSet Information",
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        "details,GeneColorSet-method",
        "details,GeneSet-method",
        "details-methods"
      ]
    },
    {
      "page": "GeneColorSet-methods",
      "title": "Methods to Construct \"GeneColorSet\" Instances",
      "topics": [
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        "GeneColorSet,BroadCollection-method",
        "GeneColorSet,character-method",
        "GeneColorSet,ExpressionSet-method",
        "GeneColorSet,GeneIdentifierType-method",
        "GeneColorSet,GeneSet-method",
        "GeneColorSet,GOCollection-method",
        "GeneColorSet,missing-method",
        "GeneColorSet-methods"
      ]
    },
    {
      "page": "GeneColorSet-class",
      "title": "Class \"GeneColorSet\"",
      "topics": [
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        "&,GeneColorSet,character-method",
        "&,GeneColorSet,GeneColorSet-method",
        "coloring",
        "coloring,GeneColorSet-method",
        "coloring<-",
        "coloring<-,GeneColorSet,data.frame-method",
        "geneColor",
        "geneColor,GeneColorSet-method",
        "geneColor<-",
        "geneColor<-,GeneColorSet,factor-method",
        "GeneColorSet-class",
        "initialize,GeneColorSet-method",
        "intersect,GeneColorSet,GeneColorSet-method",
        "phenotype",
        "phenotype,GeneColorSet-method",
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        "phenotype<-,GeneColorSet,character-method",
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        "[[,GeneColorSet,numeric-method",
        "|,GeneColorSet,character-method",
        "|,GeneColorSet,GeneColorSet-method"
      ]
    },
    {
      "page": "GeneIdentifierType-constructors",
      "title": "Gene Identifier Class Constructors",
      "topics": [
        "AnnoOrEntrezIdentifier",
        "AnnotationIdentifier",
        "ENSEMBLIdentifier",
        "EntrezIdentifier",
        "EnzymeIdentifier",
        "GeneIdentifierType",
        "GenenameIdentifier",
        "GOAllFrameIdentifier",
        "KEGGFrameIdentifier",
        "NullIdentifier",
        "RefseqIdentifier",
        "SymbolIdentifier",
        "UniprotIdentifier"
      ]
    },
    {
      "page": "GeneIdentifierType-class",
      "title": "Class \"GeneIdentifierType\"",
      "topics": [
        "annotation,GeneIdentifierType-method",
        "annotation<-,GeneIdentifierType,character-method",
        "AnnotationIdentifier-class",
        "ENSEMBLIdentifier-class",
        "EntrezIdentifier-class",
        "EnzymeIdentifier-class",
        "GeneIdentifierType-class",
        "geneIdType,GeneIdentifierType-method",
        "GenenameIdentifier-class",
        "GOAllFrameIdentifier-class",
        "initialize,GeneIdentifierType-method",
        "KEGGFrameIdentifier-class",
        "NullIdentifier-class",
        "RefseqIdentifier-class",
        "show,AnnotationIdentifier-method",
        "show,GeneIdentifierType-method",
        "SymbolIdentifier-class",
        "UniprotIdentifier-class"
      ]
    },
    {
      "page": "GeneSet-methods",
      "title": "Methods to construct GeneSet instances",
      "topics": [
        "GeneSet",
        "GeneSet,BroadCollection-method",
        "GeneSet,character-method",
        "GeneSet,ExpressionSet-method",
        "GeneSet,GeneIdentifierType-method",
        "GeneSet,GOCollection-method",
        "GeneSet,missing-method",
        "GeneSet-methods"
      ]
    },
    {
      "page": "GeneSet-class",
      "title": "Class \"GeneSet\"",
      "topics": [
        "$,GeneSet-method",
        "&,GeneSet,character-method",
        "&,GeneSet,GeneSet-method",
        "collectionType",
        "collectionType,GeneSet-method",
        "collectionType<-",
        "collectionType<-,GeneSet,CollectionType-method",
        "contributor",
        "contributor,GeneSet-method",
        "contributor<-",
        "contributor<-,GeneSet,character-method",
        "creationDate",
        "creationDate,GeneSet-method",
        "creationDate<-",
        "creationDate<-,GeneSet,character-method",
        "description,GeneSet-method",
        "description<-,GeneSet,character-method",
        "geneIds",
        "geneIds,GeneSet-method",
        "geneIds<-",
        "geneIds<-,GeneSet,character-method",
        "geneIdType",
        "geneIdType,GeneSet-method",
        "geneIdType<-",
        "geneIdType<-,GeneSet,character-method",
        "geneIdType<-,GeneSet,GeneIdentifierType-method",
        "GeneSet-class",
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        "intersect,GeneSet,GeneSet-method",
        "Logic,character,GeneSet-method",
        "longDescription",
        "longDescription,GeneSet-method",
        "longDescription<-",
        "longDescription<-,GeneSet,character-method",
        "organism",
        "organism,GeneIdentifierType-method",
        "organism,GeneSet-method",
        "organism,GOAllFrameIdentifier-method",
        "organism,KEGGFrameIdentifier-method",
        "organism<-",
        "organism<-,GeneSet,character-method",
        "pubMedIds,GeneSet-method",
        "pubMedIds<-,GeneSet,character-method",
        "setdiff,GeneSet,GeneSet-method",
        "setIdentifier",
        "setIdentifier,GeneSet-method",
        "setIdentifier<-",
        "setIdentifier<-,GeneSet,character-method",
        "setName",
        "setName,GeneSet-method",
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        "setName<-,GeneSet,character-method",
        "setVersion",
        "setVersion,GeneSet-method",
        "setVersion<-",
        "setVersion<-,GeneSet,Versions-method",
        "show,GeneSet-method",
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        "urls<-",
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        "[,ExpressionSet,GeneSet,ANY-method",
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        "[[,GeneSet,numeric-method",
        "|,GeneSet,character-method",
        "|,GeneSet,GeneSet-method"
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    {
      "page": "GeneSetCollection-class",
      "title": "Class \"GeneSetCollection\"",
      "topics": [
        "&,ANY,GeneSetCollection-method",
        "&,GeneSetCollection,ANY-method",
        "&,GeneSetCollection,GeneSetCollection-method",
        "geneIds,GeneSetCollection-method",
        "geneIds<-,GeneSetCollection,list-method",
        "GeneSetCollection-class",
        "intersect,ANY,GeneSetCollection-method",
        "intersect,GeneSetCollection,ANY-method",
        "Logic,character,GeneSetCollection-method",
        "Logic,GeneSet,GeneSetCollection-method",
        "names,GeneSetCollection-method",
        "setdiff,ANY,GeneSetCollection-method",
        "setdiff,GeneSetCollection,ANY-method",
        "show,GeneSetCollection-method",
        "toGmt,GeneSetCollection-method",
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        "union,GeneSetCollection,ANY-method",
        "updateObject,GeneSetCollection-method",
        "[,GeneSetCollection,character,ANY-method",
        "[,GeneSetCollection,logical,ANY-method",
        "[,GeneSetCollection,numeric,ANY-method",
        "[<-,GeneSetCollection,ANY,ANY,ANY-method",
        "[<-,GeneSetCollection,ANY,ANY,GeneSet-method",
        "[<-,GeneSetCollection,character,ANY,GeneSet-method",
        "[[,GeneSetCollection,character-method",
        "[[<-,GeneSetCollection,ANY,ANY,ANY-method",
        "[[<-,GeneSetCollection,character,ANY,GeneSet-method",
        "[[<-,GeneSetCollection,numeric,ANY,GeneSet-method",
        "|,ANY,GeneSetCollection-method",
        "|,GeneSetCollection,ANY-method",
        "|,GeneSetCollection,GeneSetCollection-method"
      ]
    },
    {
      "page": "GeneSetCollection-methods",
      "title": "Methods to construct GeneSetCollection instances",
      "topics": [
        "GeneSetCollection",
        "GeneSetCollection,character,AnnotationIdentifier,ChrlocCollection-method",
        "GeneSetCollection,character,AnnotationIdentifier,CollectionIdType-method",
        "GeneSetCollection,character,AnnotationIdentifier,CollectionType-method",
        "GeneSetCollection,character,AnnotationIdentifier,GOCollection-method",
        "GeneSetCollection,character,AnnotationIdentifier,PfamCollection-method",
        "GeneSetCollection,character,AnnotationIdentifier,PrositeCollection-method",
        "GeneSetCollection,ExpressionSet,missing,ChrlocCollection-method",
        "GeneSetCollection,ExpressionSet,missing,CollectionIdType-method",
        "GeneSetCollection,ExpressionSet,missing,CollectionType-method",
        "GeneSetCollection,ExpressionSet,missing,GOCollection-method",
        "GeneSetCollection,ExpressionSet,missing,KEGGCollection-method",
        "GeneSetCollection,ExpressionSet,missing,PfamCollection-method",
        "GeneSetCollection,ExpressionSet,missing,PrositeCollection-method",
        "GeneSetCollection,GeneSet,missing,missing-method",
        "GeneSetCollection,GOAllFrame,missing,GOCollection-method",
        "GeneSetCollection,KEGGFrame,missing,KEGGCollection-method",
        "GeneSetCollection,list,missing,missing-method",
        "GeneSetCollection,missing,AnnotationIdentifier,CollectionIdType-method",
        "GeneSetCollection,missing,AnnotationIdentifier,CollectionType-method",
        "GeneSetCollection,missing,AnnotationIdentifier,GOCollection-method",
        "GeneSetCollection,missing,AnnotationIdentifier,KEGGCollection-method",
        "GeneSetCollection-methods"
      ]
    },
    {
      "page": "getOBOCollection",
      "title": "Read OBO-specified Gene Ontology Collections",
      "topics": [
        "getOBOCollection"
      ]
    },
    {
      "page": "goSlim-methods",
      "title": "Methods for Function goSlim in Package `GSEABase'",
      "topics": [
        "goSlim",
        "goSlim,ExpressionSet,GOCollection-method",
        "goSlim,GOCollection,GOCollection-method",
        "goSlim-methods"
      ]
    },
    {
      "page": "getObjects",
      "title": "Read and write gene sets from Broad or GMT formats",
      "topics": [
        "asBroadUri",
        "getBroadSets",
        "getGmt",
        "io",
        "toBroadXML",
        "toGmt"
      ]
    },
    {
      "page": "incidence-methods",
      "title": "Methods for Constructing Incidence Matricies Between GeneSets",
      "topics": [
        "incidence",
        "incidence,GeneSet-method",
        "incidence,GeneSetCollection-method",
        "incidence-methods"
      ]
    },
    {
      "page": "mapIdentifiers-methods",
      "title": "Methods for Function mapIdentifiers in Package `GSEABase'",
      "topics": [
        "mapIdentifiers",
        "mapIdentifiers,ANY,ANY,ANY-method",
        "mapIdentifiers,GeneColorSet,GeneIdentifierType,AnnDbBimap-method",
        "mapIdentifiers,GeneColorSet,GeneIdentifierType,environment-method",
        "mapIdentifiers,GeneColorSet,GeneIdentifierType,GeneIdentifierType-method",
        "mapIdentifiers,GeneColorSet,GeneIdentifierType,NullIdentifier-method",
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      "page": "OBOCollection-class",
      "title": "Class \"OBOCollection\"",
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        "OBOCollection-class",
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      "filename": "GSEABase.html",
      "title": "An introduction to GSEABase",
      "author": "Martin Morgan, Paul Villafuerte",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "GeneSetCollection"
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      "created": "2023-02-24 21:10:07",
      "modified": "2023-02-24 21:10:07",
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