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  "Type": "Package",
  "Title": "Transform public data resources into Bioconductor Data\nStructures",
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  "Encoding": "UTF-8",
  "Authors@R": "c(\nperson(\"Martin\", \"Morgan\", role=\"ctb\"),\nperson(\"Marc\", \"Carlson\", role=\"ctb\"),\nperson(\"Dan\", \"Tenenbaum\", role=\"ctb\"),\nperson(\"Sonali\", \"Arora\", role=\"ctb\"),\nperson(\"Paul\", \"Shannon\", role=\"ctb\"),\nperson(\"Lori\", \"Shepherd\", role=\"ctb\"),\nperson(\"Bioconductor Package Maintainer\",\nemail=\"maintainer@bioconductor.org\", role=\"cre\")\n)",
  "Description": "These recipes convert a wide variety and a growing number\nof public bioinformatic data sets into easily-used standard\nBioconductor data structures.",
  "License": "Artistic-2.0",
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  "biocViews": "DataImport",
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  "Collate": "Message-class.R ImportPreparer-class.R\nmakeAnnotationHubResource.R HubMetadata-class.R\nAnnotationHubMetadata-class.R utils.R updateResources.R\nahmToJson.R webAccessFunctions.R makeChEA.R makedbSNPVCF.R\nmakeEncodeDCC.R makeEnsemblGtfToGRanges.R makeEnsemblFasta.R\nmakeEpigenomeRoadmap.R makeGencodeFasta.R makeGencodeGFF.R\nmakeGrasp2Db.R makeHaemCode.R makeInparanoid8ToDbs.R\nmakeNCBIToOrgDbs.R makeStandardOrgDbsToSqlite.R\nmakeStandardTxDbsToSqlite.R makeRefNet.R makeUCSCChain.R\nmakeUCSC2Bit.R makeUCSCTracks.R\ntrackWithAuxiliaryTableToGRangesRecipe.R\nUCSCTrackUpdateChecker.R makeEnsemblTwoBit.R\nvalidationFunctions.R",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:41:49 UTC",
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  "Author": "Martin Morgan [ctb],\nMarc Carlson [ctb],\nDan Tenenbaum [ctb],\nSonali Arora [ctb],\nPaul Shannon [ctb],\nLori Shepherd [ctb],\nBioconductor Package Maintainer [cre]",
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    "annotationHubRoot",
    "checkSpeciesTaxId",
    "constructSeqInfo",
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    "ensemblFastaToTwoBitFile",
    "flog",
    "gencodeFastaToFaFile",
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    "makeGencodeFastaToAHM",
    "makeNCBIToOrgDbsToAHM",
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    "UCSCTrackImportPreparer",
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    "upload_to_S3",
    "validDispatchClass",
    "validSpecies"
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    {
      "page": "AnnotationHubData-package",
      "title": "Transform public data resources into Bioconductor Data Structures",
      "topics": [
        "AnnotationHubData-package",
        "AnnotationHubRecipes"
      ]
    },
    {
      "page": "AnnotationHubMetadata-class",
      "title": "Class '\"AnnotationHubMetadata\"' and methods",
      "topics": [
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        "AnnotationHubMetadata",
        "AnnotationHubMetadata-class",
        "class:AnnotationHubMetadata",
        "class:HubMetadata",
        "constructSeqInfo",
        "deleteResources",
        "getImportPreparerClasses",
        "hubError",
        "hubError,HubMetadata-method",
        "hubError,list-method",
        "hubError<-",
        "hubError<-,HubMetadata,character-method",
        "hubError<-,list,character-method",
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        "show",
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    },
    {
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      "title": "Class 'ImportPreparer' and generic 'newResources'",
      "topics": [
        "annotationHubRoot",
        "dbSNPVCFImportPreparer",
        "dbSNPVCFImportPreparer-class",
        "EncodeImportPreparer",
        "EncodeImportPreparer-class",
        "EnsemblFastaImportPreparer",
        "EnsemblFastaImportPreparer-class",
        "EnsemblGtfImportPreparer",
        "EnsemblGtfImportPreparer-class",
        "getImportPreparer",
        "Grasp2ImportPreparer",
        "Grasp2ImportPreparer-class",
        "HaemCodeImportPreparer",
        "HaemCodeImportPreparer-class",
        "ImportPreparer-class",
        "Inparanoid8ImportPreparer",
        "Inparanoid8ImportPreparer-class",
        "metadataList",
        "metadataTable",
        "NCBIImportPreparer",
        "NCBIImportPreparer-class",
        "newResources",
        "newResources,dbSNPVCFImportPreparer-method",
        "newResources,EncodeImportPreparer-method",
        "newResources,EnsemblFastaImportPreparer-method",
        "newResources,EnsemblGtfImportPreparer-method",
        "newResources,Grasp2ImportPreparer-method",
        "newResources,HaemCodeImportPreparer-method",
        "newResources,ImportPreparer-method",
        "newResources,Inparanoid8ImportPreparer-method",
        "newResources,NCBIImportPreparer-method",
        "newResources,RefNetImportPreparer-method",
        "newResources,UCSCChainPreparer-method",
        "newResources,UCSCFullTrackImportPreparer-method",
        "newResources,UCSCTrackImportPreparer-method",
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        "show,ImportPreparer-method",
        "sourceUrls",
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        "UCSCTrackImportPreparer",
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    {
      "page": "makeAnnotationHubMetadata",
      "title": "Make AnnotationHubMetadata objects from csv file of metadata",
      "topics": [
        "makeAnnotationHubMetadata"
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    },
    {
      "page": "makeEnsemblFasta",
      "title": "Functions to convert Ensembl FASTA files to FaFile and TwoBitFile for inclusion in AnnotationHub.",
      "topics": [
        "ensemblFastaToFaFile",
        "ensemblFastaToTwoBitFile",
        "makeEnsemblFasta",
        "makeEnsemblFastaToAHM",
        "makeEnsemblTwoBitToAHM"
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    },
    {
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      "topics": [
        "gencodeFastaToFaFile",
        "makeGencodeFasta",
        "makeGencodeFastaToAHM"
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    },
    {
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      "title": "Functions to add OrgDb and TxDb sqlite files to AnnotationHub",
      "topics": [
        "makeNCBIToOrgDbsToAHM",
        "makeNonStandardOrgDbs",
        "makeStandardOrgDbs",
        "makeStandardOrgDbsToAHM",
        "makeStandardTxDbs",
        "makeStandardTxDbsToAHM"
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        "runRecipes",
        "runRecipes,AnnotationHubMetadata-method",
        "updateResources"
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    },
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      "topics": [
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        "AZURE_SAS_URL",
        "DataLake",
        "upload_to_azure"
      ]
    },
    {
      "page": "upload_to_S3",
      "title": "Upload a file to Amazon S3",
      "topics": [
        "amazon",
        "AWS",
        "S3",
        "upload_to_S3"
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    },
    {
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      "title": "ValidationFunctions",
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        "getValidSourceTypes",
        "suggestSpecies",
        "validationFunctions",
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      "filename": "IntroductionToAnnotationHubData.html",
      "title": "Introduction to AnnotationHubData",
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      "engine": "knitr::rmarkdown",
      "headings": [
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        "Creating an AnnotationHub Package or Converting to an AnnotationHub Package",
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