{
  "_id": "6a106b22acfb0bcc41caa3a7",
  "Package": "annotate",
  "Title": "Annotation for microarrays",
  "Version": "1.91.0",
  "Author": "R. Gentleman",
  "Authors@R": "c(\nperson(\"Jeff\", \"Gentry\", role = \"aut\"),\nperson(\"Kritika\", \"Verma\", role = \"ctb\",\ncomment = \"Converted chromLOC vignette from Sweave to RMarkdown / HTML.\"),\nperson(\"Manvi\", \"Yaduvanshi\", role = \"ctb\",\ncomment = \"Converted useDataPkgs vignette from Sweave to RMarkdown / HTML.\"),\nperson(\"Bioconductor Package Maintainer\",\nemail = \"maintainer@bioconductor.org\", role = \"cre\"))",
  "Description": "Using R enviroments for annotation.",
  "VignetteBuilder": "knitr",
  "License": "Artistic-2.0",
  "LazyLoad": "yes",
  "Collate": "AllGenerics.R ACCNUMStats.R Amat.R AnnMaps.R chromLocation.R\ncompatipleVersions.R findNeighbors.R getData.R getPMInfo.R\ngetSeq4ACC.R GOhelpers.R homoData.R html.R isValidKey.R\nLL2homology.R pmid2MIAME.R pubMedAbst.R query.R readGEOAnn.R\nserializeEnv.R blastSequences.R zzz.R test_annotate_package.R",
  "biocViews": "Annotation, Pathways, GO",
  "Packaged": {
    "Date": "2026-05-07 09:43:02 UTC",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:29:54 UTC",
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    "pathways",
    "go"
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    "extra/citation.cff",
    "extra/citation.html",
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    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
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  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    ".buildAnnotateOpts",
    ".efetch",
    ".getIdTag",
    ".getNcbiURL",
    ".handleXML",
    ".transformAccession",
    "abstText",
    "ACC2homology",
    "accessionToUID",
    "ACCNUMStats",
    "allValidKeys",
    "annPkgName",
    "aqListGOIDs",
    "articleTitle",
    "authors",
    "blastSequences",
    "buildChromLocation",
    "buildPubMedAbst",
    "checkArgs",
    "chrCats",
    "chromInfo",
    "chromLengths",
    "chromLocs",
    "chromNames",
    "clearRepository",
    "compatibleVersions",
    "createLLChrCats",
    "createMAPIncMat",
    "dataSource",
    "Definition",
    "dropECode",
    "entrezGeneByID",
    "entrezGeneQuery",
    "fileName",
    "filterGOByOntology",
    "findChr4LL",
    "findNeighbors",
    "genbank",
    "geneSymbols",
    "getAnnMap",
    "getBoundary",
    "getEG",
    "getEvidence",
    "getGI",
    "getGO",
    "getGOChildren",
    "getGOdesc",
    "getGOOntology",
    "getGOParents",
    "getGOTerm",
    "getGPLNames",
    "getOntology",
    "getOrgNameNCode",
    "getPMID",
    "getPMInfo",
    "getQueryLink",
    "getRepositories",
    "getSAGEFileInfo",
    "getSAGEGPL",
    "getSEQ",
    "getSYMBOL",
    "getUniqAnnItem",
    "getValidChr",
    "GO2heatmap",
    "GOID",
    "GOmnplot",
    "hasGOannote",
    "HGID2homology",
    "homoACC",
    "homoData",
    "homoHGID",
    "homoLL",
    "homoOrg",
    "homoPS",
    "homoType",
    "homoURL",
    "htmlpage",
    "initialize",
    "isValidKey",
    "journal",
    "KEGG2heatmap",
    "KEGGmnplot",
    "LL2homology",
    "lookUp",
    "mainPage",
    "makeAnchor",
    "mapOrgs",
    "nChrom",
    "Ontology",
    "organism",
    "pageText",
    "pageTitle",
    "pm.abstGrep",
    "pm.getabst",
    "pm.titles",
    "pmAbst2HTML",
    "pmid",
    "pmid2MIAME",
    "PMIDAmat",
    "pmidQuery",
    "probesToChrom",
    "pubDate",
    "pubmed",
    "pubMedAbst",
    "PWAmat",
    "readGEOAnn",
    "readIDNAcc",
    "readUrl",
    "Secondary",
    "serializeDataPkgEnvs",
    "serializeEnv",
    "setRepository",
    "show",
    "sidePage",
    "Synonym",
    "Term",
    "toFile",
    "topPage",
    "UniGeneQuery",
    "updateSymbolsToValidKeys",
    "usedChromGenes",
    "weightByConfi",
    "whatACC"
  ],
  "_datasets": [
    {
      "name": "hgByChroms",
      "title": "A dataset to show the human genome base pair locations per chromosome.",
      "object": "hgByChroms",
      "file": "hgByChroms.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "hgCLengths",
      "title": "A dataset which contains the lengths (in base pairs) of the human chromosomes.",
      "object": "hgCLengths",
      "file": "hgCLengths.rda",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "hgu95Achroloc",
      "title": "Annotation data for the Affymetrix HGU95A GeneChip",
      "object": "hgu95Achroloc",
      "file": "hgu95Achroloc.rda",
      "class": [
        "environment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "hgu95Achrom",
      "title": "Annotation data for the Affymetrix HGU95A GeneChip",
      "object": "hgu95Achrom",
      "file": "hgu95Achrom.rda",
      "class": [
        "environment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "hgu95All",
      "title": "Annotation data for the Affymetrix HGU95A GeneChip",
      "object": "hgu95All",
      "file": "hgu95All.rda",
      "class": [
        "environment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "hgu95AProbLocs",
      "title": "chromLocation instance hgu95AProbLocs, an example of a chromLocation object",
      "object": "hgu95AProbLocs",
      "file": "hgu95AProbLocs.rda",
      "class": [
        "chromLocation"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "hgu95Asym",
      "title": "Annotation data for the Affymetrix HGU95A GeneChip",
      "object": "hgu95Asym",
      "file": "hgu95Asym.rda",
      "class": [
        "environment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "accessionToUID",
      "title": "A function to convert accession values to NCBI UIDs.",
      "topics": [
        "accessionToUID"
      ]
    },
    {
      "page": "ACCNUMStats",
      "title": "Provides statistics on the types of ids used for the ACCNUM environment of a given data package",
      "topics": [
        "ACCNUMStats",
        "whatACC"
      ]
    },
    {
      "page": "annPkgName",
      "title": "Get annotation package name from chip name",
      "topics": [
        "annPkgName"
      ]
    },
    {
      "page": "aqListGOIDs",
      "title": "List GO Identifiers by GO Ontology",
      "topics": [
        "aqListGOIDs"
      ]
    },
    {
      "page": "blastSequences",
      "title": "Run a blast query to NCBI for either a string or an entrez gene ID and then return a series of MultipleAlignment objects.",
      "topics": [
        "blastSequences"
      ]
    },
    {
      "page": "buildChromLocation",
      "title": "A function to generate an instantiation of a chromLocation class",
      "topics": [
        "buildChromLocation"
      ]
    },
    {
      "page": "buildPubMedAbst",
      "title": "A function to generate an instantiation of a pubMedAbst class",
      "topics": [
        "buildPubMedAbst"
      ]
    },
    {
      "page": "chrCats",
      "title": "Returns a list of chromosome locations from a MAP environment",
      "topics": [
        "chrCats",
        "createLLChrCats",
        "createMAPIncMat"
      ]
    },
    {
      "page": "chromLocation-class",
      "title": "Class chromLocation, a class for describing genes and their chromosome mappings.",
      "topics": [
        "chromInfo",
        "chromInfo,chromLocation-method",
        "chromLengths",
        "chromLengths,chromLocation-method",
        "chromLocation",
        "chromLocation-class",
        "chromLocs",
        "chromLocs,chromLocation-method",
        "chromNames",
        "chromNames,chromLocation-method",
        "dataSource",
        "dataSource,chromLocation-method",
        "geneSymbols",
        "geneSymbols,chromLocation-method",
        "nChrom",
        "nChrom,chromLocation-method",
        "organism,chromLocation-method",
        "probesToChrom",
        "probesToChrom,chromLocation-method",
        "show,chromLocation-method"
      ]
    },
    {
      "page": "compatibleVersions",
      "title": "function to check to see if the packages represented by the names passed have the same version number",
      "topics": [
        "compatibleVersions"
      ]
    },
    {
      "page": "dropECode",
      "title": "Drop GO labels for specified Evidence Codes",
      "topics": [
        "dropECode"
      ]
    },
    {
      "page": "entrezGeneByID",
      "title": "Create a Query String for an Entrez Gene Identifier",
      "topics": [
        "entrezGeneByID"
      ]
    },
    {
      "page": "entrezGeneQuery",
      "title": "Create a Query String for Entrez Genes",
      "topics": [
        "entrezGeneQuery"
      ]
    },
    {
      "page": "filterGOByOntology",
      "title": "Filter GO terms by a specified GO ontology",
      "topics": [
        "filterGOByOntology"
      ]
    },
    {
      "page": "findNeighbors",
      "title": "A function to locate neighboring genes within a defined range around a target gene represented by a Entrez Gene ID",
      "topics": [
        "checkArgs",
        "findChr4LL",
        "findNeighbors",
        "getBoundary",
        "getValidChr",
        "weightByConfi"
      ]
    },
    {
      "page": "genbank",
      "title": "A function to open the browser to Genbank with the selected gene.",
      "topics": [
        "genbank"
      ]
    },
    {
      "page": "getAnnMap",
      "title": "Get annotation map",
      "topics": [
        "getAnnMap"
      ]
    },
    {
      "page": "getEvidence",
      "title": "Get the Evidence codes for a set of GO terms.",
      "topics": [
        "getEvidence"
      ]
    },
    {
      "page": "getGOTerm",
      "title": "Functions to Access GO data.",
      "topics": [
        "getGOChildren",
        "getGOOntology",
        "getGOParents",
        "getGOTerm"
      ]
    },
    {
      "page": "getOntology",
      "title": "Get GO terms for a specified ontology",
      "topics": [
        "getOntology"
      ]
    },
    {
      "page": "getPMInfo",
      "title": "extract publication details and abstract from annotate::pubmed function output",
      "topics": [
        "getPMInfo"
      ]
    },
    {
      "page": "getTDRows",
      "title": "Functions to create hypertext links that can be placed in a table cell of a HTML file",
      "topics": [
        "getCells",
        "getQuery4Affy",
        "getQuery4EN",
        "getQuery4ENSEMBL",
        "getQuery4FB",
        "getQuery4GB",
        "getQuery4OMIM",
        "getQuery4SP",
        "getQuery4TR",
        "getQuery4UG",
        "getQueryLink",
        "getTDRows"
      ]
    },
    {
      "page": "getSeq4Acc",
      "title": "Queries the NCBI database to obtain the sequence for a given GenBank Accession number",
      "topics": [
        "getGI",
        "getSEQ"
      ]
    },
    {
      "page": "getSYMBOL",
      "title": "Functions to deal with Data Packages",
      "topics": [
        "getEG",
        "getGO",
        "getGOdesc",
        "getPMID",
        "getSYMBOL",
        "getUniqAnnItem",
        "lookUp"
      ]
    },
    {
      "page": "GO2heatmap",
      "title": "Compute a heatmap for the specified data, for either a GO category or a KEGG pathway.",
      "topics": [
        "GO2heatmap",
        "KEGG2heatmap",
        "KEGG2heatmap,character,eSet,character-method",
        "KEGG2heatmap,character,matrix,character-method"
      ]
    },
    {
      "page": "GOmnplot",
      "title": "A function to plot by group means against each other.",
      "topics": [
        "GOmnplot",
        "KEGGmnplot",
        "KEGGmnplot,character,eSet,character-method",
        "KEGGmnplot,character,matrix,character-method"
      ]
    },
    {
      "page": "hasGOannote",
      "title": "Check for GO annotation",
      "topics": [
        "hasGOannote"
      ]
    },
    {
      "page": "hgByChroms",
      "title": "A dataset to show the human genome base pair locations per chromosome.",
      "topics": [
        "hgByChroms"
      ]
    },
    {
      "page": "hgCLengths",
      "title": "A dataset which contains the lengths (in base pairs) of the human chromosomes.",
      "topics": [
        "hgCLengths"
      ]
    },
    {
      "page": "hgu95Achroloc",
      "title": "Annotation data for the Affymetrix HGU95A GeneChip",
      "topics": [
        "hgu95Achroloc"
      ]
    },
    {
      "page": "hgu95Achrom",
      "title": "Annotation data for the Affymetrix HGU95A GeneChip",
      "topics": [
        "hgu95Achrom"
      ]
    },
    {
      "page": "hgu95All",
      "title": "Annotation data for the Affymetrix HGU95A GeneChip",
      "topics": [
        "hgu95All"
      ]
    },
    {
      "page": "hgu95AProbLocs",
      "title": "chromLocation instance hgu95AProbLocs, an example of a chromLocation object",
      "topics": [
        "hgu95AProbLocs"
      ]
    },
    {
      "page": "hgu95Asym",
      "title": "Annotation data for the Affymetrix HGU95A GeneChip",
      "topics": [
        "hgu95Asym"
      ]
    },
    {
      "page": "homoData-class",
      "title": "Class \"homoData\"",
      "topics": [
        "homoACC",
        "homoACC,homoData-method",
        "homoData",
        "homoData-class",
        "homoHGID",
        "homoHGID,homoData-method",
        "homoLL",
        "homoLL,homoData-method",
        "homoOrg",
        "homoOrg,homoData-method",
        "homoPS",
        "homoPS,homoData-method",
        "homoType",
        "homoType,homoData-method",
        "homoURL",
        "homoURL,homoData-method",
        "orgNameNCode",
        "show,homoData-method"
      ]
    },
    {
      "page": "htmlpage",
      "title": "Functions to build HTML pages",
      "topics": [
        "htmlpage"
      ]
    },
    {
      "page": "HTMLPage-class",
      "title": "Classes to represent HTML pages",
      "topics": [
        "fileName",
        "fileName,HTMLPage-method",
        "FramedHTMLPage",
        "FramedHTMLPage,HTMLPage-method",
        "FramedHTMLPage-class",
        "HTMLPage",
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        "sidePage,FramedHTMLPage-method",
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        "topPage,FramedHTMLPage-method",
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      "page": "isValidkey",
      "title": "Get or verify valid IDs for a package or OrgDb object.",
      "topics": [
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        "allValidKeys,character-method",
        "allValidKeys,OrgDb-method",
        "isValidKey",
        "isValidKey,character,character-method",
        "isValidKey,character,OrgDb-method"
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      "page": "LL2homology",
      "title": "DEFUNCT Functions that find the homology data for a given set of LocusLink ids or HomoloGeneIDs",
      "topics": [
        "ACC2homology",
        "HGID2homology",
        "LL2homology"
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    },
    {
      "page": "makeAnchor",
      "title": "A Function To Generate HTML Anchors",
      "topics": [
        "makeAnchor"
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    },
    {
      "page": "mapOrgs",
      "title": "Functions to map to organism IDs used by NCBI homology.",
      "topics": [
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        "mapOrgs"
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      "page": "pm.abstGrep",
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    },
    {
      "page": "pm.getabst",
      "title": "Obtain the abstracts for a set PubMed list.",
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      "page": "pm.titles",
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    },
    {
      "page": "pmAbst2HTML",
      "title": "HTML Generation for PubMed Abstracts",
      "topics": [
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    },
    {
      "page": "pmid2MIAME",
      "title": "use web to populate MIAME instance with pubmed details",
      "topics": [
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    },
    {
      "page": "PMIDAmat",
      "title": "A function to compute the probe to PubMed id incidence matrix.",
      "topics": [
        "PMIDAmat"
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    },
    {
      "page": "pmidQuery",
      "title": "A function to query PubMed",
      "topics": [
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    },
    {
      "page": "pubmed",
      "title": "A function to open the browser to Pubmed with the selected gene.",
      "topics": [
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    },
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      "page": "pubMedAbst-class",
      "title": "Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.",
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        "authors",
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      "page": "PWAmat",
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      "topics": [
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    },
    {
      "page": "readGEOAnn",
      "title": "Function to extract data from the GEO web site",
      "topics": [
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        "getSAGEGPL",
        "readGEOAnn",
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    {
      "page": "serializeEnv",
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      "topics": [
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        "serializeEnv"
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    },
    {
      "page": "setRepository",
      "title": "Functions to add arbitrary repositories",
      "topics": [
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    },
    {
      "page": "UniGeneQuery",
      "title": "Create a Query String for a UniGene Identifier",
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      "page": "updateSymbolsToValidKeys",
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    },
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      "page": "usedChromGenes",
      "title": "A function to select used genes on a chromosome from an ExpressionSet.",
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