{
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  "Package": "Category",
  "Title": "Category Analysis",
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  "Authors@R": "c(\nperson(\"Robert\", \"Gentleman\", role=\"aut\"),\nperson(\"Seth\", \"Falcon\", role=\"ctb\"),\nperson(\"Deepayan\", \"Sarkar\", role=\"ctb\"),\nperson(\"Robert\", \"Castelo\", role=\"ctb\"),\nperson(\"Bioconductor Package Maintainer\",\nemail = \"maintainer@bioconductor.org\", role=\"cre\"))",
  "Description": "A collection of tools for performing category (gene set\nenrichment) analysis.",
  "License": "Artistic-2.0",
  "LazyLoad": "Yes",
  "Collate": "AllClasses.R AllGenerics.R categoryToEntrezBuilder-methods.R\ncategoryName-methods.R hyperg-methods.R hyperGTest-methods.R\nlinearMTest-methods.R DatPkg-accessors.R ChrBandTree.R\ntree_visitor.R cb_test.R initialize-methods.R\nHyperGParams-accessors.R LinearMParams-accessors.R\nHyperGResult-accessors.R LinearMResult-accessors.R\nChrMapHyperGResult-accessors.R ChrMapLinearMResult-accessors.R\nshow-methods.R universeBuilder-methods.R utils.R MAPcode.R\ncatcode.R cateGOryMatrix.R gseaperm.R summary-methods.R mouse.R",
  "biocViews": "Annotation, GO, Pathways, GeneSetEnrichment",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:31:12 UTC",
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  "Author": "Robert Gentleman [aut],\nSeth Falcon [ctb],\nDeepayan Sarkar [ctb],\nRobert Castelo [ctb],\nBioconductor Package Maintainer [cre]",
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    "pathways",
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  "_exports": [
    ".doHyperGTest",
    "allGeneIds",
    "annotation",
    "annotation<-",
    "applyByCategory",
    "cateGOry",
    "categoryName",
    "categoryToEntrezBuilder",
    "cb_children",
    "cb_contingency",
    "cb_parse_band_Hs",
    "cb_parse_band_Mm",
    "cb_sigBands",
    "cb_test",
    "childrenOf",
    "ChrBandTreeFromGraph",
    "chrGraph",
    "conditional",
    "conditional<-",
    "DatPkgFactory",
    "description",
    "effectSize",
    "exampleLevels",
    "expectedCounts",
    "findAMstats",
    "geneCounts",
    "geneIds",
    "geneIds<-",
    "geneIdsByCategory",
    "geneIdUniverse",
    "geneMappedCount",
    "getPathNames",
    "GO2AllProbes",
    "GSEAGOHyperGParams",
    "GSEAKEGGHyperGParams",
    "gseattperm",
    "htmlReport",
    "hyperg",
    "hyperGTest",
    "ID2EntrezID",
    "ID2GO",
    "ID2KEGG",
    "initialize",
    "KEGG2AllProbes",
    "level2nodes",
    "lgeneIds",
    "linearMTest",
    "makeChrBandGraph",
    "makeChrBandGSC",
    "makeChrBandInciMat",
    "makeEBcontr",
    "makeValidParams",
    "MAPAmat",
    "NewChrBandTree",
    "OBOCollectionDatPkg",
    "OBOHyperGParams",
    "oddsRatios",
    "ontology",
    "ontology<-",
    "organism",
    "parentOf",
    "probes2MAP",
    "probes2Path",
    "pvalueCutoff",
    "pvalueCutoff<-",
    "pvalues",
    "show",
    "sigCategories",
    "summary",
    "testDirection",
    "testDirection<-",
    "testName",
    "treeLevels",
    "ttperm",
    "universeBuilder",
    "universeCounts",
    "universeGeneIds",
    "universeMappedCount"
  ],
  "_help": [
    {
      "page": "applyByCategory",
      "title": "Apply a function to a vector of statistics, by category",
      "topics": [
        "applyByCategory"
      ]
    },
    {
      "page": "cateGOryMatrix",
      "title": "Construct a category membership matrix from a list of gene identifiers and their annotated GO categories.",
      "topics": [
        "cateGOry"
      ]
    },
    {
      "page": "Category-defunct",
      "title": "Defunct Functions in Package 'Category'",
      "topics": [
        "Category-defunct",
        "cb_parse_band_hsa",
        "chrBandInciMat",
        "condGeneIdUniverse",
        "geneGoHyperGeoTest",
        "geneKeggHyperGeoTest",
        "isConditional"
      ]
    },
    {
      "page": "categoryToEntrezBuilder",
      "title": "Return a list mapping category ids to Entrez Gene ids",
      "topics": [
        "categoryToEntrezBuilder",
        "categoryToEntrezBuilder,GOHyperGParams-method",
        "categoryToEntrezBuilder,KEGGHyperGParams-method",
        "categoryToEntrezBuilder,OBOHyperGParams-method",
        "categoryToEntrezBuilder,PFAMHyperGParams-method"
      ]
    },
    {
      "page": "cb_contingency",
      "title": "Create and Test Contingency Tables of Chromosome Band Annotations",
      "topics": [
        "cb_children",
        "cb_contingency",
        "cb_sigBands"
      ]
    },
    {
      "page": "cb_parse_band_Hs",
      "title": "Parse Homo Sapiens Chromosome Band Annotations",
      "topics": [
        "cb_parse_band_Hs"
      ]
    },
    {
      "page": "cb_parse_band_Mm",
      "title": "Parse Mus Musculus Chromosome Band Annotations",
      "topics": [
        "cb_parse_band_Mm"
      ]
    },
    {
      "page": "cb_test",
      "title": "Chromosome Band Tree-Based Hypothesis Testing",
      "topics": [
        "cb_test"
      ]
    },
    {
      "page": "ChrBandTree-class",
      "title": "Class \"ChrBandTree\"",
      "topics": [
        "allGeneIds",
        "allGeneIds,ChrBandTree-method",
        "childrenOf",
        "childrenOf,ChrBandTree,character-method",
        "ChrBandTree-class",
        "geneIds,ChrBandTree-method",
        "level2nodes",
        "level2nodes,ChrBandTree,character-method",
        "level2nodes,ChrBandTree,numeric-method",
        "lgeneIds",
        "lgeneIds,ChrBandTree-method",
        "parentOf",
        "parentOf,ChrBandTree,character-method",
        "show,ChrBandTree-method",
        "treeLevels",
        "treeLevels,ChrBandTree-method"
      ]
    },
    {
      "page": "ChrMapHyperGParams-class",
      "title": "Class \"ChrMapHyperGParams\"",
      "topics": [
        "ChrMapHyperGParams-class",
        "conditional,ChrMapHyperGParams-method",
        "conditional<-,ChrMapHyperGParams,logical-method"
      ]
    },
    {
      "page": "ChrMapHyperGResult-class",
      "title": "Class \"ChrMapHyperGResult\"",
      "topics": [
        "ChrMapHyperGResult-class",
        "conditional,ChrMapHyperGResult-method"
      ]
    },
    {
      "page": "ChrMapLinearMParams-class",
      "title": "Class \"ChrMapLinearMParams\"",
      "topics": [
        "ChrMapLinearMParams-class"
      ]
    },
    {
      "page": "ChrMapLinearMResult-class",
      "title": "Class \"ChrMapLinearMResult\"",
      "topics": [
        "chrGraph,ChrMapLinearMResult-method",
        "ChrMapLinearMResult-class"
      ]
    },
    {
      "page": "DatPkg-class",
      "title": "Class \"DatPkg\"",
      "topics": [
        "AffyDatPkg-class",
        "ArabidopsisDatPkg-class",
        "DatPkg-class",
        "DatPkgFactory",
        "DatPkgFactory,character-method",
        "DatPkgFactory,ChipDb-method",
        "DatPkgFactory,OBOCollection,GeneSetCollection-method",
        "DatPkgFactory,OrgDb-method",
        "GeneSetCollectionDatPkg",
        "GO2AllProbes",
        "GO2AllProbes,DatPkg-method",
        "GO2AllProbes,GeneSetCollectionDatPkg-method",
        "GO2AllProbes,Org.XX.egDatPkg-method",
        "GO2AllProbes,YeastDatPkg-method",
        "ID2EntrezID",
        "ID2EntrezID,AffyDatPkg-method",
        "ID2EntrezID,ArabidopsisDatPkg-method",
        "ID2EntrezID,GeneSetCollectionDatPkg-method",
        "ID2EntrezID,Org.XX.egDatPkg-method",
        "ID2EntrezID,YeastDatPkg-method",
        "ID2GO",
        "ID2GO,DatPkg-method",
        "ID2GO,GeneSetCollectionDatPkg-method",
        "ID2KEGG",
        "ID2KEGG,DatPkg-method",
        "ID2KEGG,GeneSetCollectionDatPkg-method",
        "isDBDatPkg,DatPkg-method",
        "isDBDatPkg,GeneSetCollectionDatPkg-method",
        "KEGG2AllProbes",
        "KEGG2AllProbes,DatPkg-method",
        "KEGG2AllProbes,GeneSetCollectionDatPkg-method",
        "OBOCollectionDatPkg",
        "OBOCollectionDatPkg-class",
        "Org.XX.egDatPkg-class",
        "organism,DatPkg-method",
        "organism,GeneSetCollectionDatPkg-method",
        "YeastDatPkg-class"
      ]
    },
    {
      "page": "effectSize",
      "title": "Extract estimated effect sizes",
      "topics": [
        "effectSize"
      ]
    },
    {
      "page": "exampleLevels",
      "title": "Display a sample node from each level of a ChrBandTree object",
      "topics": [
        "exampleLevels"
      ]
    },
    {
      "page": "findAMstats",
      "title": "Compute per category summary statistics",
      "topics": [
        "findAMstats"
      ]
    },
    {
      "page": "getPathNames",
      "title": "A function to print pathway names given their numeric ID.",
      "topics": [
        "getPathNames"
      ]
    },
    {
      "page": "GOHyperGParams-class",
      "title": "Class \"GOHyperGParams\"",
      "topics": [
        "annotation,GOHyperGParams-method",
        "categoryName,GOHyperGParams-method",
        "conditional,GOHyperGParams-method",
        "conditional<-,GOHyperGParams,logical-method",
        "GOHyperGParams-class",
        "ontology,GOHyperGParams-method",
        "ontology<-,GOHyperGParams,character-method",
        "show,GOHyperGParams-method"
      ]
    },
    {
      "page": "GSEAGOHyperGParams",
      "title": "Helper function for constructing a GOHyperGParams objects or KEGGHyperGParams objects from a GeneSetCollection",
      "topics": [
        "GSEAGOHyperGParams",
        "GSEAKEGGHyperGParams"
      ]
    },
    {
      "page": "gseattperm",
      "title": "Permutation p-values for GSEA",
      "topics": [
        "gseattperm"
      ]
    },
    {
      "page": "hyperg",
      "title": "Hypergeometric (gene set enrichment) tests on character vectors.",
      "topics": [
        "hyperg",
        "hyperg,character-method",
        "hyperg,list-method"
      ]
    },
    {
      "page": "HyperGParams-class",
      "title": "Class \"HyperGParams\"",
      "topics": [
        "annotation,HyperGParams-method",
        "annotation<-,HyperGParams,character-method",
        "categoryName",
        "categoryName,HyperGParams-method",
        "conditional",
        "conditional,HyperGParams-method",
        "conditional<-",
        "geneIds,HyperGParams-method",
        "geneIds<-",
        "geneIds<-,HyperGParams,ANY-method",
        "geneIds<-,HyperGParams,logical-method",
        "HyperGParams-class",
        "initialize,HyperGParams-method",
        "makeValidParams,HyperGParams-method",
        "ontology",
        "ontology,HyperGParams-method",
        "ontology<-",
        "organism,HyperGParams-method",
        "pvalueCutoff,HyperGParams-method",
        "pvalueCutoff<-",
        "pvalueCutoff<-,HyperGParams-method",
        "show,HyperGParams-method",
        "testDirection,HyperGParams-method",
        "testDirection<-",
        "testDirection<-,HyperGParams-method",
        "universeGeneIds",
        "universeGeneIds,HyperGParams-method"
      ]
    },
    {
      "page": "HyperGResult-accessors",
      "title": "Accessors for HyperGResult Objects",
      "topics": [
        "annotation",
        "annotation,HyperGResultBase-method",
        "chrGraph",
        "chrGraph,ChrMapHyperGResult-method",
        "description",
        "description,HyperGResultBase-method",
        "expectedCounts",
        "expectedCounts,ChrMapHyperGResult-method",
        "expectedCounts,HyperGResult-method",
        "geneCounts",
        "geneCounts,HyperGResultBase-method",
        "geneIds",
        "geneIds,HyperGResultBase-method",
        "geneIdsByCategory",
        "geneIdsByCategory,HyperGResultBase-method",
        "geneIdUniverse",
        "geneIdUniverse,ChrMapHyperGResult-method",
        "geneIdUniverse,HyperGResult-method",
        "geneMappedCount",
        "geneMappedCount,HyperGResultBase-method",
        "htmlReport",
        "htmlReport,HyperGResultBase-method",
        "htmlReport,KEGGHyperGResult-method",
        "htmlReport,PFAMHyperGResult-method",
        "HyperGResult-accessors",
        "oddsRatios",
        "oddsRatios,ChrMapHyperGResult-method",
        "oddsRatios,HyperGResult-method",
        "organism,HyperGResult-method",
        "pvalueCutoff",
        "pvalueCutoff,HyperGResultBase-method",
        "pvalues",
        "pvalues,ChrMapHyperGResult-method",
        "pvalues,HyperGResult-method",
        "sigCategories",
        "sigCategories,HyperGResultBase-method",
        "summary,HyperGResultBase-method",
        "summary,KEGGHyperGResult-method",
        "summary,PFAMHyperGResult-method",
        "testDirection",
        "testDirection,HyperGResultBase-method",
        "testName",
        "testName,HyperGResultBase-method",
        "universeCounts",
        "universeCounts,HyperGResultBase-method",
        "universeMappedCount",
        "universeMappedCount,HyperGResultBase-method"
      ]
    },
    {
      "page": "HyperGResult-class",
      "title": "Class \"HyperGResult\"",
      "topics": [
        "HyperGResult-class",
        "KEGGHyperGResult-class",
        "PFAMHyperGResult-class"
      ]
    },
    {
      "page": "HyperGResultBase-class",
      "title": "Class \"HyperGResultBase\"",
      "topics": [
        "conditional,HyperGResultBase-method",
        "HyperGResultBase-class",
        "show,HyperGResultBase-method"
      ]
    },
    {
      "page": "hyperGTest",
      "title": "Hypergeometric Test for association of categories and genes",
      "topics": [
        "hyperGTest",
        "hyperGTest,ChrMapHyperGParams-method",
        "hyperGTest,HyperGParams-method",
        "hyperGTest,KEGGHyperGParams-method",
        "hyperGTest,PFAMHyperGParams-method"
      ]
    },
    {
      "page": "KEGGHyperGParams-class",
      "title": "Class \"KEGGHyperGParams\" and \"PFAMHyperGParams\"",
      "topics": [
        "KEGGHyperGParams-class",
        "PFAMHyperGParams-class"
      ]
    },
    {
      "page": "LinearMParams-class",
      "title": "Class \"LinearMParams\"",
      "topics": [
        "annotation,LinearMParams-method",
        "annotation<-,LinearMParams,character-method",
        "categoryName,LinearMParams-method",
        "conditional,LinearMParams-method",
        "conditional<-,LinearMParams,logical-method",
        "geneIds,LinearMParams-method",
        "geneIds<-,LinearMParams,ANY-method",
        "LinearMParams-class",
        "pvalueCutoff,LinearMParams-method",
        "pvalueCutoff<-,LinearMParams-method",
        "show,LinearMParams-method",
        "testDirection,LinearMParams-method",
        "testDirection<-,LinearMParams-method",
        "universeGeneIds,LinearMParams-method"
      ]
    },
    {
      "page": "LinearMResult-class",
      "title": "Class \"LinearMResult\"",
      "topics": [
        "effectSize,LinearMResult-method",
        "LinearMResult-class",
        "pvalues,LinearMResult-method",
        "summary,LinearMResult-method"
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      "title": "Class \"LinearMResultBase\"",
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        "conditional,LinearMResultBase-method",
        "description,LinearMResultBase-method",
        "geneIds,LinearMResultBase-method",
        "geneIdsByCategory,LinearMResultBase-method",
        "geneIdUniverse,LinearMResultBase-method",
        "geneMappedCount,LinearMResultBase-method",
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        "sigCategories,LinearMResultBase-method",
        "summary,LinearMResultBase-method",
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      "page": "linearMTest",
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      "topics": [
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    },
    {
      "page": "makeChrBandGraph",
      "title": "Create a graph representing chromosome band annotation data",
      "topics": [
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    },
    {
      "page": "makeEBcontr",
      "title": "A function to make the contrast vectors needed for EBarrays",
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    },
    {
      "page": "makeValidParams",
      "title": "Non-standard Generic for Checking Validity of Parameter Objects",
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    },
    {
      "page": "MAPAmat",
      "title": "Mapping chromosome bands to genes",
      "topics": [
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        "makeChrBandInciMat",
        "MAPAmat"
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    },
    {
      "page": "NewChrBandTree",
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        "NewChrBandTree"
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    },
    {
      "page": "probes2MAP",
      "title": "Map probe IDs to MAP regions.",
      "topics": [
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    },
    {
      "page": "probes2Path",
      "title": "A function to map probe identifiers to pathways.",
      "topics": [
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    },
    {
      "page": "ttperm",
      "title": "A simple function to compute a permutation t-test.",
      "topics": [
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    },
    {
      "page": "universeBuilder",
      "title": "Return a vector of gene identifiers with category annotations",
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        "universeBuilder,OBOHyperGParams-method",
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    "mime",
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    "pkgconfig",
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    "R6",
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    "S4Vectors",
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  "_indexed": true,
  "_nocasepkg": "category",
  "_universes": [
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