{
  "_id": "6a494f7af6c47c441949a716",
  "Package": "cellbaseR",
  "Type": "Package",
  "Date": "2016-04-17",
  "Title": "Querying annotation data from the high performance Cellbase web",
  "Version": "1.37.0",
  "Author": "Mohammed OE Abdallah",
  "Maintainer": "Mohammed OE Abdallah <melsiddieg@gmail.com>",
  "URL": "https://github.com/melsiddieg/cellbaseR",
  "Description": "This R package makes use of the exhaustive RESTful Web\nservice API that has been implemented for the Cellabase\ndatabase. It enable researchers to query and obtain a wealth of\nbiological information from a single database saving a lot of\ntime. Another benefit is that researchers can easily make\nqueries about different biological topics and link all this\ninformation together as all information is integrated.",
  "License": "Apache License (== 2.0)",
  "RoxygenNote": "7.2.3",
  "biocViews": "Annotation, VariantAnnotation",
  "Lazy": "TRUE",
  "Encoding": "UTF-8",
  "Collate": "'commons.R' 'AllClasses.R' 'AllGenerics.R'\n'AnnotateVcf-methods.R' 'CellBaseParam-methods.R'\n'CellBaseR-methods.R' 'cellbase.R' 'getCellbase-methods.R'\n'getChromosomeInfo-methods.R' 'getClinical-methods.R'\n'getGene-methods.R' 'getMeta-methods.R' 'getProtein-methods.R'\n'getRegion-methods.R' 'getTranscript-methods.R'\n'getVariant-methods.R' 'getXref-methods.R' 'show-methods.R'\n'tools.R' 'user.R'",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libbz2-dev libicu-dev liblzma-dev libssl-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:45:35 UTC",
  "RemoteUrl": "https://github.com/bioc/cellbaseR",
  "RemoteRef": "HEAD",
  "RemoteSha": "01b61c7a0e509ed9ac824497cf27001167db7642",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-02 07:28:36 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "cellbaseR_1.37.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/bac06f95673a3775310eef4b49c26b858540389821b1e5fec3e4d42768b09595",
  "_filesize": 447383,
  "_sha256": "bac06f95673a3775310eef4b49c26b858540389821b1e5fec3e4d42768b09595",
  "_expires": "2026-10-12T18:22:48.000Z",
  "_created": "2026-07-02T07:28:36.000Z",
  "_published": "2026-07-04T18:22:50.388Z",
  "_bioccheck": {
    "error": 1,
    "warning": 1,
    "note": 12
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28572878790",
  "_status": "success",
  "_upstream": "https://github.com/bioc/cellbaseR",
  "_commit": {
    "id": "01b61c7a0e509ed9ac824497cf27001167db7642",
    "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": 1777380335
  },
  "_maintainer": {
    "name": "Mohammed OE Abdallah",
    "email": "melsiddieg@gmail.com",
    "login": "melsiddieg",
    "description": "Post-Doctoral Fellow, Bioinformatician\nCentre for Molecular Medicine and Therapeutics, University of British Columbia",
    "uuid": 8942470
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85155947778,
      "time": 194,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8031852995"
    },
    {
      "job": 85155947712,
      "time": 318,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8031893792"
    },
    {
      "job": 85155947620,
      "time": 308,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8031890685"
    },
    {
      "job": 85155947634,
      "time": 143,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8031904064"
    },
    {
      "job": 85155947677,
      "time": 217,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8031923148"
    },
    {
      "job": 85155947478,
      "time": 282,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8031785333"
    },
    {
      "job": 85155947770,
      "time": 196,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8031854037"
    },
    {
      "job": 85155947722,
      "time": 169,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8031844383"
    },
    {
      "job": 85155947834,
      "time": 190,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8031851575"
    },
    {
      "job": 85155947776,
      "time": 164,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8031843270"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "httr",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "pbapply",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "R.utils",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "Gviz",
      "role": "Suggests"
    },
    {
      "package": "VariantAnnotation",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.37.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.36.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "annotation",
    "variantannotation"
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "imedina",
      "count": 586,
      "uuid": 1427327
    },
    {
      "user": "javild",
      "count": 386,
      "uuid": 5476132
    },
    {
      "user": "melsiddieg",
      "count": 213,
      "uuid": 8942470
    },
    {
      "user": "swaathik",
      "count": 89,
      "uuid": 15231894
    },
    {
      "user": "pabarcgar",
      "count": 67,
      "uuid": 2338089
    },
    {
      "user": "marnau",
      "count": 53,
      "uuid": 4922686
    },
    {
      "user": "frasator",
      "count": 23,
      "uuid": 1344072
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "mbleda",
      "count": 14,
      "uuid": 1344027
    },
    {
      "user": "j-coll",
      "count": 10,
      "uuid": 4750611
    },
    {
      "user": "antonior26",
      "count": 8,
      "uuid": 5476137
    },
    {
      "user": "jwokaty",
      "count": 6,
      "uuid": 1744257
    },
    {
      "user": "jperflo",
      "count": 5,
      "uuid": 9279156
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "mbsimonovic",
      "count": 1,
      "uuid": 888008
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 444,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://github.com/melsiddieg/cellbaser",
  "_searchresults": 13,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/cellbaseR.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/melsiddieg/cellbaser",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "AnnotateVcf",
    "CellBaseParam",
    "CellBaseR",
    "createGeneModel",
    "getCellBase",
    "getCellBaseResourceHelp",
    "getChromosomeInfo",
    "getClinical",
    "getConservationByRegion",
    "getGene",
    "getGeneInfo",
    "getMeta",
    "getProtein",
    "getProteinInfo",
    "getRegion",
    "getRegulatoryByRegion",
    "getTranscript",
    "getTranscriptByGene",
    "getVariant",
    "getVariantAnnotation",
    "getXref"
  ],
  "_help": [
    {
      "page": "cellbaseR-package",
      "title": "cellbaseR",
      "topics": [
        "cellbaseR-package",
        "cellbaseR"
      ]
    },
    {
      "page": "AnnotateVcf-CellBaseR-method",
      "title": "AnnotateVcf",
      "topics": [
        "AnnotateVcf",
        "AnnotateVcf,CellBaseR-method"
      ]
    },
    {
      "page": "CellBaseParam",
      "title": "A Constructor for the CellBaseParam Object",
      "topics": [
        "CellBaseParam"
      ]
    },
    {
      "page": "CellBaseParam-class",
      "title": "CellBaseParam Class",
      "topics": [
        "CellBaseParam-class"
      ]
    },
    {
      "page": "CellBaseR",
      "title": "CellBaseR",
      "topics": [
        "CellBaseR"
      ]
    },
    {
      "page": "CellBaseR-class",
      "title": "CellBaseR Class",
      "topics": [
        "CellBaseR-class"
      ]
    },
    {
      "page": "createGeneModel",
      "title": "createGeneModel",
      "topics": [
        "createGeneModel"
      ]
    },
    {
      "page": "getCellBase-CellBaseR-method",
      "title": "getCellBase",
      "topics": [
        "getCellBase",
        "getCellBase,CellBaseR-method"
      ]
    },
    {
      "page": "getCellBaseResourceHelp",
      "title": "getCellBaseResourceHelp",
      "topics": [
        "getCellBaseResourceHelp"
      ]
    },
    {
      "page": "getChromosomeInfo-CellBaseR-method",
      "title": "getChromosomeInfo",
      "topics": [
        "getChromosomeInfo",
        "getChromosomeInfo,CellBaseR-method"
      ]
    },
    {
      "page": "getClinical-CellBaseR-method",
      "title": "getClinical",
      "topics": [
        "getClinical",
        "getClinical,CellBaseR-method"
      ]
    },
    {
      "page": "getConservationByRegion",
      "title": "getConservationByRegion",
      "topics": [
        "getConservationByRegion"
      ]
    },
    {
      "page": "getGene-CellBaseR-method",
      "title": "getGene",
      "topics": [
        "getGene",
        "getGene,CellBaseR-method"
      ]
    },
    {
      "page": "getGeneInfo",
      "title": "getGeneInfo",
      "topics": [
        "getGeneInfo"
      ]
    },
    {
      "page": "getMeta-CellBaseR-method",
      "title": "getMeta",
      "topics": [
        "getMeta",
        "getMeta,CellBaseR-method"
      ]
    },
    {
      "page": "getProtein-CellBaseR-method",
      "title": "getProtein",
      "topics": [
        "getProtein",
        "getProtein,CellBaseR-method"
      ]
    },
    {
      "page": "getProteinInfo",
      "title": "getProteinInfo",
      "topics": [
        "getProteinInfo"
      ]
    },
    {
      "page": "getRegion-CellBaseR-method",
      "title": "getRegion",
      "topics": [
        "getRegion",
        "getRegion,CellBaseR-method"
      ]
    },
    {
      "page": "getRegulatoryByRegion",
      "title": "getRegulatoryByRegion",
      "topics": [
        "getRegulatoryByRegion"
      ]
    },
    {
      "page": "getTranscript-CellBaseR-method",
      "title": "getTranscript",
      "topics": [
        "getTranscript",
        "getTranscript,CellBaseR-method"
      ]
    },
    {
      "page": "getTranscriptByGene",
      "title": "getTranscriptByGene",
      "topics": [
        "getTranscriptByGene"
      ]
    },
    {
      "page": "getVariant-CellBaseR-method",
      "title": "getVariant",
      "topics": [
        "getVariant",
        "getVariant,CellBaseR-method"
      ]
    },
    {
      "page": "getVariantAnnotation",
      "title": "getVariantAnnotation",
      "topics": [
        "getVariantAnnotation"
      ]
    },
    {
      "page": "getXref-CellBaseR-method",
      "title": "getXref",
      "topics": [
        "getXref",
        "getXref,CellBaseR-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/cellbaseR/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "BH",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "doParallel",
    "dplyr",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "glue",
    "httr",
    "IRanges",
    "iterators",
    "jsonlite",
    "lambda.r",
    "lifecycle",
    "magrittr",
    "mime",
    "openssl",
    "pbapply",
    "pillar",
    "pkgconfig",
    "purrr",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "Rhtslib",
    "rlang",
    "Rsamtools",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "cellbaseR.Rmd",
      "filename": "cellbaseR.html",
      "title": "Simplifying Genomic Annotations in R",
      "author": "Mohammed Omar Elsiddieg Abdallah",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction to CellbaseR",
        "CellbaseR Classes and Methods",
        "The CellbaseR class",
        "The CellbaseR Methods",
        "getGene",
        "getRegion",
        "getVariant",
        "getClinical",
        "cellbaseR wrappers",
        "CellbaseR utilities",
        "CreateGeneModel",
        "AnnotateVcf"
      ],
      "created": "2017-10-08 19:54:35",
      "modified": "2023-11-23 05:36:54",
      "commits": 7
    }
  ],
  "_score": 5.5910646070264995,
  "_indexed": true,
  "_nocasepkg": "cellbaser",
  "_universes": [
    "bioc",
    "melsiddieg"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.37.0",
      "date": "2026-07-02T07:32:58.000Z",
      "distro": "resolute",
      "commit": "01b61c7a0e509ed9ac824497cf27001167db7642",
      "fileid": "https://r2.ropensci.org/9678d239ca7afbb53cc8af091073836d08ed0fc1f2fe46c9129d455ae8a35868",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28572878790"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.37.0",
      "date": "2026-07-02T07:32:53.000Z",
      "distro": "resolute",
      "commit": "01b61c7a0e509ed9ac824497cf27001167db7642",
      "fileid": "https://r2.ropensci.org/1feb6369af0ac95099ee460572d42c598bc11a66042c7fcc161a79e1e99ce3a1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28572878790"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.37.0",
      "date": "2026-07-02T07:33:54.000Z",
      "commit": "01b61c7a0e509ed9ac824497cf27001167db7642",
      "fileid": "https://r2.ropensci.org/37625a32d405eb5b0c347353bbf77216d46bce5fba959e9902fdf0e8a66b15f1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28572878790"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.37.0",
      "date": "2026-07-02T07:34:21.000Z",
      "commit": "01b61c7a0e509ed9ac824497cf27001167db7642",
      "fileid": "https://r2.ropensci.org/7e5240a724fa46a7258558ced69c3640ceb859716f1109007b1c12481d6467ff",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28572878790"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.37.0",
      "date": "2026-07-02T07:32:17.000Z",
      "commit": "01b61c7a0e509ed9ac824497cf27001167db7642",
      "fileid": "https://r2.ropensci.org/0f54493dd8f464bb64e9d20d50353c5c29dc74a501302e36e9e2f8ee3251ee73",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28572878790"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-07-02T07:30:14.000Z",
      "commit": "01b61c7a0e509ed9ac824497cf27001167db7642",
      "fileid": "https://r2.ropensci.org/22c945899b8980d205f58a1517a9bfe7b6b332f64cbe0d848e0540c6747fb83a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28572878790"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-07-02T07:30:28.000Z",
      "commit": "01b61c7a0e509ed9ac824497cf27001167db7642",
      "fileid": "https://r2.ropensci.org/c61e8e7820eb2b85a4a2b15957ebfa6e58b39938f6568f51ef42031849cf1672",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28572878790"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-07-02T07:30:16.000Z",
      "commit": "01b61c7a0e509ed9ac824497cf27001167db7642",
      "fileid": "https://r2.ropensci.org/b25790fc598e4f7193836a97d29d368bbbcd44dee16dc5e8590d4b98efa14a92",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28572878790"
    }
  ]
}