{
  "_id": "6a444737c375b2cc78b7711e",
  "Package": "AnnotationHub",
  "Type": "Package",
  "Title": "Client to access AnnotationHub resources",
  "Version": "4.3.2",
  "Authors@R": "c(person(\"Bioconductor Package\", \"Maintainer\", email=\"maintainer@bioconductor.org\",\nrole=\"cre\"),\nperson(\"Martin\", \"Morgan\", role=\"aut\"),\nperson(\"Marc\", \"Carlson\", role=\"ctb\"),\nperson(\"Dan\", \"Tenenbaum\", role=\"ctb\"),\nperson(\"Sonali\", \"Arora\", role=\"ctb\"),\nperson(\"Valerie\", \"Oberchain\", role=\"ctb\"),\nperson(\"Kayla\", \"Morrell\", role=\"ctb\"),\nperson(\"Lori\", \"Shepherd\", role=\"aut\"))",
  "biocViews": "Infrastructure, DataImport, GUI, ThirdPartyClient",
  "Description": "This package provides a client for the Bioconductor\nAnnotationHub web resource. The AnnotationHub web resource\nprovides a central location where genomic files (e.g., VCF,\nbed, wig) and other resources from standard locations (e.g.,\nUCSC, Ensembl) can be discovered. The resource includes\nmetadata about each resource, e.g., a textual description,\ntags, and date of modification. The client creates and manages\na local cache of files retrieved by the user, helping with\nquick and reproducible access.",
  "License": "Artistic-2.0",
  "Collate": "AnnotationHubOption.R AllGenerics.R Hub-class.R db-utils.R\nAnnotationHub-class.R AnnotationHubResource-class.R\nBEDResource-class.R ProteomicsResource-class.R\nEpigenomeResource-class.R EnsDbResource-class.R utilities.R\nsql-utils.R Hub-utils.R cache-utils.R zzz.R",
  "VignetteBuilder": "knitr",
  "BugReports": "https://github.com/Bioconductor/AnnotationHub/issues",
  "NeedsCompilation": "yes",
  "RoxygenNote": "7.3.2",
  "Config/pak/sysreqs": "libicu-dev libpng-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-06-30 17:36:56 UTC",
  "RemoteUrl": "https://github.com/bioc/AnnotationHub",
  "RemoteRef": "HEAD",
  "RemoteSha": "b406e89030efd8e164f2c00f6ece5ec98ee4301d",
  "Packaged": {
    "Date": "2026-06-30 22:39:12 UTC",
    "User": "root"
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  "Author": "Bioconductor Package Maintainer [cre],\nMartin Morgan [aut],\nMarc Carlson [ctb],\nDan Tenenbaum [ctb],\nSonali Arora [ctb],\nValerie Oberchain [ctb],\nKayla Morrell [ctb],\nLori Shepherd [aut]",
  "Maintainer": "Bioconductor Package Maintainer <maintainer@bioconductor.org>",
  "MD5sum": "6a0d7e62e91bdd28968d9abcc424a78f",
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  "_created": "2026-06-30T22:39:12.000Z",
  "_published": "2026-06-30T22:46:15.330Z",
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_devurl": "https://github.com/bioconductor/annotationhub",
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    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/bioconductor/annotationhub",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
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    ".DollarNames.Hub",
    ".getProxyValue",
    ".Hub",
    ".hub_option_key",
    "AnnotationHub",
    "as.list",
    "as.list.Hub",
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    "convertHub",
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    "dbfile",
    "DispatchClassList",
    "fileName",
    "getAnnotationHubOption",
    "getHub",
    "getInfoOnIds",
    "hubCache",
    "hubDate",
    "hubUrl",
    "isLocalHub",
    "isLocalHub<-",
    "listResources",
    "loadResources",
    "mcols",
    "package",
    "possibleDates",
    "query",
    "recordStatus",
    "refreshHub",
    "removeCache",
    "removeResources",
    "setAnnotationHubOption",
    "show",
    "snapshotDate",
    "snapshotDate<-",
    "subset"
  ],
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    {
      "page": "AnnotationHub-package",
      "title": "Light-weight AnnotationHub 3.0 Client",
      "topics": [
        "AnnotationHub-package"
      ]
    },
    {
      "page": "AnnotationHub-class",
      "title": "AnnotationHub objects and their related methods and functions",
      "topics": [
        "$,Hub-method",
        ".db_close",
        ".Hub",
        "AnnotationHub",
        "AnnotationHub-class",
        "as.list,Hub-method",
        "as.list.Hub",
        "c,Hub-method",
        "cache",
        "cache,AnnotationHub-method",
        "cache,Hub-method",
        "cache<-",
        "cache<-,Hub-method",
        "class:AnnotationHub",
        "class:Hub",
        "dbconn,Hub-method",
        "dbfile,Hub-method",
        "fileName,Hub-method",
        "Hub-class",
        "hubCache",
        "hubCache,Hub-method",
        "hubDate",
        "hubDate,Hub-method",
        "hubUrl",
        "hubUrl,Hub-method",
        "isLocalHub",
        "isLocalHub,Hub-method",
        "isLocalHub<-",
        "isLocalHub<-,Hub-method",
        "length,Hub-method",
        "mcols,Hub-method",
        "names,Hub-method",
        "package",
        "package,Hub-method",
        "possibleDates",
        "query",
        "query,Hub-method",
        "recordStatus",
        "recordStatus,Hub-method",
        "refreshHub",
        "removeCache",
        "removeResources",
        "removeResources,character-method",
        "removeResources,missing-method",
        "show,AnnotationHubResource-method",
        "show,Hub-method",
        "snapshotDate",
        "snapshotDate,Hub-method",
        "snapshotDate<-",
        "snapshotDate<-,Hub-method",
        "subset,Hub-method",
        "[,Hub,character,missing-method",
        "[,Hub,logical,missing-method",
        "[,Hub,numeric,missing-method",
        "[<-,Hub,character,missing,Hub-method",
        "[<-,Hub,logical,missing,Hub-method",
        "[<-,Hub,numeric,missing,Hub-method",
        "[[,Hub,character,missing-method",
        "[[,Hub,numeric,missing-method"
      ]
    },
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      "page": "convertHub",
      "title": "Convert old Hub to new Hub structure",
      "topics": [
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      ]
    },
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      "page": "getAnnotationHubOption",
      "title": "Get and set options for default AnnotationHub behavior.",
      "topics": [
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        "setAnnotationHubOption"
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        "getInfoOnIds,character-method",
        "getInfoOnIds,missing-method",
        "getInfoOnIds,numeric-method",
        "Hub-utils"
      ]
    },
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      "title": "Utility functions for discovering package-specific Hub resources.",
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        "listResources",
        "loadResources",
        "utilities"
      ]
    },
    {
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      "title": "Utility function to list currently available dispatchClass.",
      "topics": [
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        "utils"
      ]
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      "headings": [
        "AnnotationHub objects",
        "Interactive retrieval of resources with BiocHubsShiny",
        "Using AnnotationHub to retrieve data",
        "Configuring AnnotationHub objects",
        "AnnotationHub objects in a cluster environment",
        "Creating an AnnotationHub Package or Converting to an AnnotationHub Package",
        "Troubleshooting",
        "Accessing Behind A Proxy",
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        "Session info"
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      "modified": "2025-05-15 17:05:30",
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      "filename": "AnnotationHub-HOWTO.html",
      "title": "AnnotationHub How-To's",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Accessing Genome-Scale Data",
        "Non-model organism gene annotations",
        "Roadmap Epigenomics Project",
        "Ensembl GTF and FASTA files for TxDb gene models and sequence queries",
        "liftOver to map between genome builds",
        "sessionInfo"
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      "created": "2015-05-20 23:45:12",
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      "title": "Troubleshoot The Hubs",
      "author": "Lori Shepherd",
      "engine": "knitr::rmarkdown",
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        "Troubleshooting",
        "Accessing Behind A Proxy",
        "Other configuration options for resource downloading",
        "Invalid Cache",
        "Corrupt Cache",
        "sqlite file",
        "redownload of sqlite file",
        "index file",
        "resource path",
        "resource id",
        "Corrupt Database",
        "Cannot retrieve resource",
        "Offline localHub usage",
        "Group Hub/Cache Access",
        "Lock file Troubleshooting",
        "Permissions",
        "Cannot lock file / no lock available",
        "Default Caching Location Update",
        "Option 1: Move cache and files to new location",
        "Option 2:  Create a system environment variable",
        "Option 3: Delete the old cache"
      ],
      "created": "2023-12-11 16:07:47",
      "modified": "2025-05-15 17:05:30",
      "commits": 3
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