{
  "_id": "6a493e5ea19c9318096e7b00",
  "Package": "biocViews",
  "Title": "Categorized views of R package repositories",
  "Description": "Infrastructure to support 'views' used to classify\nBioconductor packages. 'biocViews' are directed acyclic graphs\nof terms from a controlled vocabulary. There are three major\nclassifications, corresponding to 'software', 'annotation', and\n'experiment data' packages.",
  "biocViews": "Infrastructure",
  "URL": "http://bioconductor.org/packages/biocViews",
  "BugReports": "https://github.com/Bioconductor/biocViews/issues",
  "Version": "1.81.0",
  "License": "Artistic-2.0",
  "Authors@R": "c(\nperson(\"Vincent\", \"Carey\", role = \"aut\"),\nperson(\"Benjamin\", \"Harshfield\", role = \"aut\"),\nperson(\"Seth\", \"Falcon\", role = \"aut\"),\nperson(\"Sonali\", \"Arora\", role = \"aut\"),\nperson(\"Lori\", \"Shepherd\", role = \"aut\"),\nperson(\"Bioconductor Package\", \"Maintainer\", ,\n\"maintainer@bioconductor.org\", \"cre\"))",
  "Collate": "AllClasses.R AllGenerics.R as-methods.R htmlDoc-methods.R\nhtmlFilename-methods.R htmlValue-methods.R show-methods.R\ngetPackNames.R packageDetails.R pump.R repository.R showvoc.R\ngetPackageNEWS.R validation_tests.R recommendBiocViews.R\ndump_concept.R build_dbs.R",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.2",
  "Encoding": "UTF-8",
  "Config/pak/sysreqs": "make libxml2-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:31:21 UTC",
  "RemoteUrl": "https://github.com/bioc/biocViews",
  "RemoteRef": "HEAD",
  "RemoteSha": "472ce5b9e962b1baa49843d069671dd51fe16841",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-04 03:29:00 UTC",
    "User": "root"
  },
  "Author": "Vincent Carey [aut],\nBenjamin Harshfield [aut],\nSeth Falcon [aut],\nSonali Arora [aut],\nLori Shepherd [aut],\nBioconductor Package Maintainer [cre]",
  "Maintainer": "Bioconductor Package Maintainer <maintainer@bioconductor.org>",
  "_user": "bioc",
  "_type": "src",
  "_file": "biocViews_1.81.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/15e121c51838b8322add8fca44d98b3d38b2bc090f1826a99bf1735b52516398",
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  "_expires": "2026-10-12T17:09:48.000Z",
  "_created": "2026-07-04T03:29:00.000Z",
  "_published": "2026-07-04T17:09:50.379Z",
  "_bioccheck": {
    "error": 1,
    "warning": 4,
    "note": 16
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28693458106",
  "_status": "success",
  "_upstream": "https://github.com/bioc/biocViews",
  "_commit": {
    "id": "472ce5b9e962b1baa49843d069671dd51fe16841",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777379481
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  "_maintainer": {
    "name": "Bioconductor Package Maintainer",
    "email": "maintainer@bioconductor.org",
    "login": "bioconductor-bot",
    "description": "",
    "uuid": 11681645
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  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "graph",
      "version": ">= 1.9.26",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "RBGL",
      "version": ">= 1.13.5",
      "role": "Imports"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "XML",
      "role": "Imports"
    },
    {
      "package": "RCurl",
      "role": "Imports"
    },
    {
      "package": "RUnit",
      "role": "Imports"
    },
    {
      "package": "BiocManager",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    },
    {
      "package": "BiocPkgTools",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "commonmark",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 15,
  "_updates": [
    {
      "week": "2025-36",
      "n": 8
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
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    },
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    },
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      "n": 2
    },
    {
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    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.81.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.80.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "infrastructure",
    "bioconductor-package",
    "core-package"
  ],
  "_stars": 4,
  "_contributors": [
    {
      "user": "dtenenba",
      "count": 120,
      "uuid": 2286826
    },
    {
      "user": "lshep",
      "count": 62,
      "uuid": 18724380
    },
    {
      "user": "sonali-bioc",
      "count": 52,
      "uuid": 6373953
    },
    {
      "user": "hpages",
      "count": 35,
      "uuid": 8810451
    },
    {
      "user": "jwokaty",
      "count": 31,
      "uuid": 1744257
    },
    {
      "user": "vjcitn",
      "count": 28,
      "uuid": 4624066
    },
    {
      "user": "link-ny",
      "count": 20,
      "uuid": 4392950
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "pshannon-bioc",
      "count": 4,
      "uuid": 2285629
    },
    {
      "user": "aoles",
      "count": 3,
      "uuid": 6545356
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "mcarlsn",
      "count": 1,
      "uuid": 105299892
    },
    {
      "user": "villafup",
      "count": 1,
      "uuid": 95894130
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 4,
  "_devurl": "https://github.com/bioconductor/biocviews",
  "_searchresults": 45,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/biocViews.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/bioconductor/biocviews",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "build_db_from_source",
    "build_meta_aliases_db",
    "build_meta_rdxrefs_db",
    "coerce",
    "dump_concept",
    "extractCitations",
    "extractHTMLDocuments",
    "extractManuals",
    "extractNEWS",
    "extractTopLevelFiles",
    "extractVignettes",
    "genReposControlFiles",
    "getBiocSubViews",
    "getBiocViews",
    "getCurrentbiocViews",
    "getPackageNEWS",
    "getSubTerms",
    "guessPackageType",
    "htmlDoc",
    "htmlFilename",
    "htmlValue",
    "printNEWS",
    "recommendBiocViews",
    "recommendPackages",
    "show",
    "validate_bioc_views",
    "write_REPOSITORY",
    "write_SYMBOLS",
    "write_VIEWS",
    "writeBiocViews",
    "writeHtmlDoc",
    "writePackageDetailHtml",
    "writeRepositoryHtml",
    "writeRFilesFromVignettes",
    "writeTopLevelView"
  ],
  "_datasets": [
    {
      "name": "biocViewsVocab",
      "title": "Bioconductor Task Views Vocabulary Data",
      "object": "biocViewsVocab",
      "file": "biocViewsVocab.rda",
      "class": [
        "graphNEL"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "biocViews-package",
      "title": "Categorized views of R package repositories",
      "topics": [
        "biocViews-package",
        "biocViews"
      ]
    },
    {
      "page": "BiocView-class",
      "title": "Class \"BiocView\"",
      "topics": [
        "BiocView-class",
        "bvPackageTable-class",
        "bvParentViews-class",
        "bvSubViews-class",
        "bvTitle-class",
        "coerce,BiocView,rdPackageTable-method",
        "htmlDoc,BiocView-method",
        "htmlFilename,BiocView-method",
        "htmlValue,BiocView-method",
        "htmlValue,bvParentViews-method",
        "htmlValue,bvSubViews-method",
        "show,BiocView-method"
      ]
    },
    {
      "page": "biocViewsVocab",
      "title": "Bioconductor Task Views Vocabulary Data",
      "topics": [
        "biocViewsVocab"
      ]
    },
    {
      "page": "build-dbs",
      "title": "Helper functions to generate HTML pages for reference manuals",
      "topics": [
        "build-dbs",
        "build_db_from_source",
        "build_meta_aliases_db",
        "build_meta_rdxrefs_db"
      ]
    },
    {
      "page": "dump_concept",
      "title": "produce character stream for use with Protege entities/class hierarchy ingestion based on biocViews subgraphs",
      "topics": [
        "dump_concept"
      ]
    },
    {
      "page": "extractManuals",
      "title": "Extract Rd man pages and build pdf reference manuals from local package repository",
      "topics": [
        "extractCitations",
        "extractManuals"
      ]
    },
    {
      "page": "extractNEWS",
      "title": "Extract NEWS files from source package tarballs",
      "topics": [
        "extractNEWS"
      ]
    },
    {
      "page": "extractTopLevelFiles",
      "title": "Extract files from the top level of source package tarballs",
      "topics": [
        "extractTopLevelFiles"
      ]
    },
    {
      "page": "extractVignettes",
      "title": "Extract pdf vignettes from local package repository",
      "topics": [
        "extractHTMLDocuments",
        "extractVignettes"
      ]
    },
    {
      "page": "genReposControlFiles",
      "title": "Generate CRAN-style repository control files",
      "topics": [
        "genReposControlFiles"
      ]
    },
    {
      "page": "getBiocSubViews",
      "title": "Build a list of BiocView objects from a package repository",
      "topics": [
        "getBiocSubViews"
      ]
    },
    {
      "page": "getBiocViews",
      "title": "Build a list of BiocView objects from a package repository",
      "topics": [
        "getBiocViews"
      ]
    },
    {
      "page": "getCurrentbiocViews",
      "title": "Get a list of biocViews for each branch",
      "topics": [
        "getCurrentbiocViews"
      ]
    },
    {
      "page": "getPackageNEWS",
      "title": "Retrieve and print package NEWS",
      "topics": [
        "getPackageNEWS",
        "printNEWS"
      ]
    },
    {
      "page": "getPackageTitles",
      "title": "Retrieve list of package titles and print package Description",
      "topics": [
        "getPackageDescriptions",
        "getPackageTitles"
      ]
    },
    {
      "page": "getPacksAndViews",
      "title": "Parse VIEWS file for views and packages",
      "topics": [
        "getPacksAndViews",
        "makeVocInfo",
        "permulist",
        "pump",
        "tellSubTop",
        "tellSuperTop"
      ]
    },
    {
      "page": "getSubTerms",
      "title": "Retrieve a term and its children from a vocab DAG",
      "topics": [
        "getSubTerms"
      ]
    },
    {
      "page": "guessPackageType",
      "title": "Guess Package Type (Software, ExperimentData, AnnotationData) using existing biocViews.",
      "topics": [
        "guessPackageType"
      ]
    },
    {
      "page": "htmlDoc",
      "title": "Create a complete HTML document representation of an object",
      "topics": [
        "htmlDoc"
      ]
    },
    {
      "page": "htmlFilename",
      "title": "Return a filename for an object's HTML representation",
      "topics": [
        "htmlFilename",
        "htmlFilename,character-method"
      ]
    },
    {
      "page": "Htmlized-class",
      "title": "Class \"Htmlized\"",
      "topics": [
        "htmlDoc,Htmlized-method",
        "Htmlized-class"
      ]
    },
    {
      "page": "htmlValue",
      "title": "HTML Representation of an Object",
      "topics": [
        "htmlValue"
      ]
    },
    {
      "page": "PackageDetail-class",
      "title": "Class \"PackageDetail\"",
      "topics": [
        "htmlDoc,PackageDetail-method",
        "htmlFilename,PackageDetail-method",
        "htmlValue,PackageDetail-method",
        "htmlValue,pdAuthorMaintainerInfo-method",
        "htmlValue,pdDescriptionInfo-method",
        "htmlValue,pdDetailsInfo-method",
        "htmlValue,pdDownloadInfo-method",
        "htmlValue,pdVignetteInfo-method",
        "htmlValue,pdVigsAndDownloads-method",
        "PackageDetail-class",
        "pdAuthorMaintainerInfo-class",
        "pdDescriptionInfo-class",
        "pdDetailsInfo-class",
        "pdDownloadInfo-class",
        "pdVignetteInfo-class",
        "pdVigsAndDownloads-class"
      ]
    },
    {
      "page": "recommendBiocViews",
      "title": "Recommend biocViews for an existing Package.",
      "topics": [
        "recommendBiocViews"
      ]
    },
    {
      "page": "recommendPackages",
      "title": "Recommend Packages using existing biocViews.",
      "topics": [
        "recommendPackages"
      ]
    },
    {
      "page": "RepositoryDetail-class",
      "title": "Class \"RepositoryDetail\"",
      "topics": [
        "htmlDoc,RepositoryDetail-method",
        "htmlFilename,RepositoryDetail-method",
        "htmlValue,rdPackageTable-method",
        "htmlValue,RepositoryDetail-method",
        "rdPackageTable-class",
        "RepositoryDetail-class"
      ]
    },
    {
      "page": "validation_tests",
      "title": "Validate a package's biocViews.",
      "topics": [
        "validate_bioc_views",
        "validation_tests"
      ]
    },
    {
      "page": "write_REPOSITORY",
      "title": "Write a REPOSITORY control file for a CRAN-style package repository",
      "topics": [
        "write_REPOSITORY"
      ]
    },
    {
      "page": "write_SYMBOLS",
      "title": "Write a SYMBOLS file",
      "topics": [
        "write_SYMBOLS"
      ]
    },
    {
      "page": "write_VIEWS",
      "title": "Write a VIEWS control file for a CRAN-style package repository",
      "topics": [
        "write_VIEWS"
      ]
    },
    {
      "page": "writeBiocViews",
      "title": "Write a list of BiocView objects to HTML",
      "topics": [
        "writeBiocViews"
      ]
    },
    {
      "page": "writeHtmlDoc",
      "title": "Write an XML DOM containing HTML to a file",
      "topics": [
        "writeHtmlDoc"
      ]
    },
    {
      "page": "writePackageDetailHtml",
      "title": "Write HTML files for packages in a CRAN-style repository",
      "topics": [
        "writePackageDetailHtml"
      ]
    },
    {
      "page": "writeRepositoryHtml",
      "title": "Write package descriptions and a repository index as HTML",
      "topics": [
        "writeRepositoryHtml"
      ]
    },
    {
      "page": "writeRFilesFromVignettes",
      "title": "Write R files from vignettes",
      "topics": [
        "writeRFilesFromVignettes"
      ]
    },
    {
      "page": "writeTopLevelView",
      "title": "Write the view for the root of a vocabulary to disk",
      "topics": [
        "writeTopLevelView"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/biocViews/raw/HEAD/README.md",
  "_rundeps": [
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocManager",
    "bitops",
    "generics",
    "graph",
    "RBGL",
    "RCurl",
    "RUnit",
    "XML"
  ],
  "_vignettes": [
    {
      "source": "createReposHtml.Rmd",
      "filename": "createReposHtml.html",
      "title": "HOWTO generate repository HTML",
      "author": "S. Falcon",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "CRAN-style Layout",
        "Extracting vignettes",
        "Generating the control files",
        "Generating the HTML",
        "Design and extension notes",
        "Details on HTML generation",
        "A note on the htmlValue method for PackageDetail"
      ],
      "created": "2022-08-03 00:33:56",
      "modified": "2022-08-03 00:33:56",
      "commits": 1
    },
    {
      "source": "HOWTO-BCV.Rmd",
      "filename": "HOWTO-BCV.html",
      "title": "HOWTO generate biocViews HTML",
      "author": "S. Falcon and V.J. Carey",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Establishing a vocabulary of terms",
        "Use Case: adding a term to the vocabulary",
        "Use Case: updating BioConductor website",
        "Querying a repository",
        "Generating HTML"
      ],
      "created": "2022-08-03 00:46:04",
      "modified": "2022-08-03 00:46:04",
      "commits": 1
    }
  ],
  "_score": 9.492816243246182,
  "_indexed": true,
  "_nocasepkg": "biocviews",
  "_universes": [
    "bioc",
    "bioconductor-bot",
    "bioconductor"
  ],
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