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  "Package": "AnnotationDbi",
  "Title": "Manipulation of SQLite-based annotations in Bioconductor",
  "Description": "Implements a user-friendly interface for querying\nSQLite-based annotation data packages.",
  "biocViews": "Annotation, Microarray, Sequencing, GenomeAnnotation",
  "URL": "https://bioconductor.org/packages/AnnotationDbi",
  "Video": "https://www.youtube.com/watch?v=8qvGNTVz3Ik",
  "BugReports": "https://github.com/Bioconductor/AnnotationDbi/issues",
  "Version": "1.75.0",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "Author": "Hervé Pagès, Marc Carlson, Seth Falcon, Nianhua Li",
  "Maintainer": "Bioconductor Package Maintainer\n<maintainer@bioconductor.org>",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:32:03 UTC",
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    "as.list",
    "as.list.Bimap",
    "checkMAPCOUNTS",
    "chooseCentralOrgPkgSymbol",
    "colmetanames",
    "colnames",
    "columns",
    "contents",
    "count.links",
    "count.mappedkeys",
    "count.mappedLkeys",
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    "createAnnObjs.SchemaChoice",
    "createSimpleBimap",
    "dbconn",
    "dbfile",
    "dbFileConnect",
    "dbFileDisconnect",
    "dbGetTable",
    "dbInfo",
    "dbmeta",
    "dbschema",
    "debugSQL",
    "Definition",
    "direction",
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    "exists",
    "filterSeeds",
    "get",
    "getBimapFilters",
    "getGOFrameData",
    "getKEGGFrameData",
    "getOrgPkgForSchema",
    "GOAllFrame",
    "GOFrame",
    "GOID",
    "GOTerms",
    "hasMultiProbes",
    "hasSingleProbes",
    "head",
    "idConverter",
    "initialize",
    "inpIDMapper",
    "intraIDMapper",
    "isNA",
    "KEGGFrame",
    "keyname",
    "keys",
    "keys<-",
    "keytypes",
    "links",
    "Lkeyname",
    "Lkeys",
    "Lkeys<-",
    "Llength",
    "loadDb",
    "ls",
    "make_eg_to_go_map",
    "make_go_to_eg_map",
    "makeGOGraph",
    "mapIds",
    "mapIds_base",
    "mappedkeys",
    "mappedLkeys",
    "mappedRkeys",
    "mergeToNamespaceAndExport",
    "metadata",
    "mget",
    "NCBICHIP_DB_SeedGenerator",
    "ncol",
    "nhit",
    "nrow",
    "Ontology",
    "organismKEGGFrame",
    "orgPackageName",
    "Rattribnames",
    "Rattribnames<-",
    "resort_base",
    "revmap",
    "Rkeyname",
    "Rkeys",
    "Rkeys<-",
    "Rlength",
    "sample",
    "saveDb",
    "Secondary",
    "select",
    "show",
    "showQCData",
    "species",
    "subset",
    "summary",
    "Synonym",
    "tagname",
    "tail",
    "taxonomyId",
    "Term",
    "testForValidKeytype",
    "testSelectArgs",
    "toggleProbes",
    "toSQLStringSet",
    "toTable",
    "unlist2"
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      "title": "Descriptions of available values for 'columns' and 'keytypes'.",
      "topics": [
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        "ALIAS",
        "ARACYC",
        "ARACYCENZYME",
        "CHR",
        "CHRLOC",
        "CHRLOCEND",
        "COMMON",
        "DESCRIPTION",
        "ENSEMBL",
        "ENSEMBLPROT",
        "ENSEMBLTRANS",
        "ENTREZID",
        "ENZYME",
        "EVIDENCE",
        "EVIDENCEALL",
        "GENENAME",
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        "INTERPRO",
        "IPI",
        "MAP",
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        "ONTOLOGYALL",
        "ORF",
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        "SMART",
        "SYMBOL",
        "TAIR",
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        "UNIPROT"
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    {
      "page": "AnnDbObj-class",
      "title": "AnnDbObj objects",
      "topics": [
        "AnnDbObj",
        "AnnDbObj-class",
        "AnnDbObj-objects",
        "class:AnnDbObj",
        "dbconn",
        "dbconn,AnnDbObj-method",
        "dbconn,environment-method",
        "dbconn,SQLiteConnection-method",
        "dbfile",
        "dbfile,AnnDbObj-method",
        "dbfile,environment-method",
        "dbfile,SQLiteConnection-method",
        "dbInfo",
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        "dbInfo,DBIConnection-method",
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        "dbmeta,DBIConnection-method",
        "dbmeta,environment-method",
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        "dbschema,AnnDbObj-method",
        "dbschema,DBIConnection-method",
        "dbschema,environment-method"
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    },
    {
      "page": "AnnDbPkg-checker",
      "title": "Check the SQL data contained in an SQLite-based annotation package",
      "topics": [
        "AnnDbPkg-checker",
        "checkMAPCOUNTS"
      ]
    },
    {
      "page": "AnnotationDb-class",
      "title": "AnnotationDb objects and their progeny, methods etc.",
      "topics": [
        "AnnotationDb",
        "AnnotationDb-class",
        "ChipDb-class",
        "class:AnnotationDb",
        "cols",
        "columns",
        "columns,AnnotationDb-method",
        "columns,ChipDb-method",
        "columns,GODb-method",
        "columns,Inparanoid8Db-method",
        "columns,InparanoidDb-method",
        "columns,OrgDb-method",
        "columns,OrthologyDb-method",
        "columns,ReactomeDb-method",
        "dbconn,AnnotationDb-method",
        "dbfile,AnnotationDb-method",
        "GODb-class",
        "InparanoidDb-class",
        "keys",
        "keys,ChipDb-method",
        "keys,GODb-method",
        "keys,Inparanoid8Db-method",
        "keys,InparanoidDb-method",
        "keys,OrgDb-method",
        "keys,OrthologyDb-method",
        "keys,ReactomeDb-method",
        "keytypes",
        "keytypes,ChipDb-method",
        "keytypes,GODb-method",
        "keytypes,Inparanoid8Db-method",
        "keytypes,InparanoidDb-method",
        "keytypes,OrgDb-method",
        "keytypes,OrthologyDb-method",
        "keytypes,ReactomeDb-method",
        "loadDb",
        "mapIds",
        "mapIds,AnnotationDb-method",
        "metadata,AnnotationDb-method",
        "names,AnnotationDb-method",
        "OrgDb-class",
        "OrthologyDb-class",
        "ReactomeDb-class",
        "saveDb",
        "saveDb,AnnotationDb-method",
        "select",
        "select,ChipDb-method",
        "select,GODb-method",
        "select,Inparanoid8Db-method",
        "select,InparanoidDb-method",
        "select,OrgDb-method",
        "select,OrthologyDb-method",
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        "species",
        "species,AnnotationDb-method",
        "taxonomyId",
        "taxonomyId,AnnotationDb-method"
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      "title": "Bimap objects and the Bimap interface",
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        "AgiAnnDbMap-class",
        "AnnDbBimap",
        "AnnDbBimap-class",
        "AnnDbMap",
        "AnnDbMap-class",
        "Bimap",
        "Bimap-class",
        "class:AgiAnnDbMap",
        "class:AnnDbBimap",
        "class:AnnDbMap",
        "class:Bimap",
        "class:Go3AnnDbBimap",
        "class:GoAnnDbBimap",
        "class:GOTermsAnnDbBimap",
        "class:IpiAnnDbMap",
        "class:ProbeAnnDbBimap",
        "class:ProbeAnnDbMap",
        "class:ProbeGo3AnnDbBimap",
        "class:ProbeIpiAnnDbMap",
        "Go3AnnDbBimap",
        "Go3AnnDbBimap-class",
        "GoAnnDbBimap",
        "GoAnnDbBimap-class",
        "GOTermsAnnDbBimap",
        "GOTermsAnnDbBimap-class",
        "IpiAnnDbMap",
        "IpiAnnDbMap-class",
        "ProbeAnnDbBimap",
        "ProbeAnnDbBimap-class",
        "ProbeAnnDbMap",
        "ProbeAnnDbMap-class",
        "ProbeGo3AnnDbBimap",
        "ProbeGo3AnnDbBimap-class",
        "ProbeIpiAnnDbMap",
        "ProbeIpiAnnDbMap-class",
        "show,AnnDbBimap-method",
        "show,FlatBimap-method",
        "summary,AnnDbBimap-method",
        "summary,Bimap-method"
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      "topics": [
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        "count.mappedLkeys",
        "count.mappedLkeys,AgiAnnDbMap-method",
        "count.mappedLkeys,AnnDbBimap-method",
        "count.mappedLkeys,Bimap-method",
        "count.mappedLkeys,Go3AnnDbBimap-method",
        "count.mappedRkeys",
        "count.mappedRkeys,AnnDbBimap-method",
        "count.mappedRkeys,AnnDbMap-method",
        "count.mappedRkeys,Bimap-method",
        "count.mappedRkeys,Go3AnnDbBimap-method",
        "direction",
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        "direction,FlatBimap-method",
        "direction<-",
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        "direction<-,AnnDbMap-method",
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        "Lkeys,AnnDbBimap-method",
        "Lkeys,FlatBimap-method",
        "Lkeys,ProbeAnnDbBimap-method",
        "Lkeys,ProbeAnnDbMap-method",
        "Lkeys,ProbeGo3AnnDbBimap-method",
        "Lkeys,ProbeIpiAnnDbMap-method",
        "Lkeys<-",
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        "Llength,ProbeGo3AnnDbBimap-method",
        "Llength,ProbeIpiAnnDbMap-method",
        "mappedLkeys",
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        "mappedLkeys,AnnDbBimap-method",
        "mappedLkeys,FlatBimap-method",
        "mappedLkeys,Go3AnnDbBimap-method",
        "mappedRkeys",
        "mappedRkeys,AnnDbBimap-method",
        "mappedRkeys,AnnDbMap-method",
        "mappedRkeys,FlatBimap-method",
        "mappedRkeys,Go3AnnDbBimap-method",
        "revmap",
        "revmap,AnnDbBimap-method",
        "revmap,Bimap-method",
        "revmap,environment-method",
        "revmap,list-method",
        "Rkeys",
        "Rkeys,AnnDbBimap-method",
        "Rkeys,AnnDbMap-method",
        "Rkeys,FlatBimap-method",
        "Rkeys,Go3AnnDbBimap-method",
        "Rkeys<-",
        "Rkeys<-,AnnDbBimap-method",
        "Rkeys<-,FlatBimap-method",
        "Rlength",
        "Rlength,AnnDbBimap-method",
        "Rlength,AnnDbMap-method",
        "Rlength,Bimap-method",
        "Rlength,Go3AnnDbBimap-method",
        "subset,AnnDbBimap-method",
        "subset,Bimap-method"
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      "page": "Bimap-envirAPI",
      "title": "Environment-like API for Bimap objects",
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        "Bimap-envirAPI",
        "contents,Bimap-method",
        "eapply",
        "eapply,Bimap-method",
        "exists",
        "exists,ANY,ANY,Bimap-method",
        "exists,ANY,Bimap,missing-method",
        "get",
        "get,ANY,ANY,Bimap-method",
        "get,ANY,Bimap,missing-method",
        "ls",
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        "mget,Bimap-method",
        "sample",
        "sample,Bimap-method",
        "sample,environment-method",
        "[[,Bimap-method"
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      "page": "Bimap-keys",
      "title": "Methods for manipulating the keys of a Bimap object",
      "topics": [
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        "count.mappedkeys",
        "count.mappedkeys,ANY-method",
        "count.mappedkeys,Bimap-method",
        "isNA",
        "isNA,ANY-method",
        "isNA,Bimap-method",
        "isNA,environment-method",
        "keys,Bimap-method",
        "keys<-",
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        "length,Bimap-method",
        "mappedkeys",
        "mappedkeys,Bimap-method",
        "mappedkeys,environment-method",
        "mappedkeys,vector-method",
        "show,AnnDbTable-method",
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      "page": "Bimap-toTable",
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        "as.data.frame.Bimap",
        "Bimap-toTable",
        "colmetanames",
        "colmetanames,AnnDbBimap-method",
        "colmetanames,FlatBimap-method",
        "colnames",
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        "colnames,FlatBimap-method",
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        "links",
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        "links,Bimap-method",
        "links,FlatBimap-method",
        "links,Go3AnnDbBimap-method",
        "Lkeyname",
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        "Lkeyname,Bimap-method",
        "ncol",
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        "nhit",
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        "nhit,environment-method",
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        "nrow,AnnDbTable-method",
        "nrow,Bimap-method",
        "nrow,FlatBimap-method",
        "nrow,Go3AnnDbBimap-method",
        "Rattribnames",
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        "Rattribnames,Bimap-method",
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        "tail,FlatBimap-method",
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        "toTable,Bimap-method",
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        "as.list,Bimap-method",
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    },
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      "page": "GOFrame",
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        "class:GOFrame",
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        "getGOFrameData,GOAllFrame-method",
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      "page": "GOTerms-class",
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      "page": "inpIDMapper",
      "title": "Convenience functions for mapping IDs through an appropriate set of annotation packages",
      "topics": [
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    {
      "page": "KEGGFrame",
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        "getKEGGFrameData",
        "getKEGGFrameData,KEGGAllFrame-method",
        "getKEGGFrameData,KEGGFrame-method",
        "KEGGFrame",
        "KEGGFrame,data.frame,character-method",
        "KEGGFrame,data.frame,missing-method",
        "KEGGFrame-class"
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    },
    {
      "page": "make_eg_to_go_map",
      "title": "Create GO to Entrez Gene maps for chip-based packages",
      "topics": [
        "make_eg_to_go_map",
        "make_go_to_eg_map"
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    },
    {
      "page": "makeGOGraph",
      "title": "A convenience function to generate graphs based on the GO.db package",
      "topics": [
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    {
      "page": "organismKEGGFrame",
      "title": "A data frame that maps species names to KEGG organisms",
      "topics": [
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      "page": "orgPackageName",
      "title": "Org package contained in annotation object",
      "topics": [
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    {
      "page": "print.probetable",
      "title": "Print method for probetable objects",
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      "page": "BimapFiltering",
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      "topics": [
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      "page": "toSQLStringSet",
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      "page": "unlist2",
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