{
  "_id": "6a1ad0991d7bb097a09e1842",
  "Package": "GenomicDataCommons",
  "Type": "Package",
  "Title": "NIH / NCI Genomic Data Commons Access",
  "Description": "Programmatically access the NIH / NCI Genomic Data Commons\nRESTful service.",
  "Version": "1.37.0",
  "Date": "2025-05-12",
  "Authors@R": "c( person(\"Martin\", \"Morgan\",\nemail=\"martin.morgan@roswellpark.org\", role=c(\"aut\")),\nperson(\"Sean\", \"Davis\", email=\"seandavi@gmail.com\",\nrole=c(\"aut\", \"cre\")),\nperson(\"Marcel\", \"Ramos\",\nemail = \"marcel.ramos@sph.cuny.edu\", role = \"ctb\"))",
  "License": "Artistic-2.0",
  "biocViews": "DataImport, Sequencing",
  "URL": "https://bioconductor.org/packages/GenomicDataCommons,\nhttp://github.com/Bioconductor/GenomicDataCommons,\nhttp://bioconductor.github.io/GenomicDataCommons/",
  "BugReports": "https://github.com/Bioconductor/GenomicDataCommons/issues/new",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.2",
  "Config/pak/sysreqs": "libicu-dev libxml2-dev libssl-dev libx11-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:45:25 UTC",
  "RemoteUrl": "https://github.com/bioc/GenomicDataCommons",
  "RemoteRef": "HEAD",
  "RemoteSha": "1f1dd57f36ddcd76f4b53c80e81ae993c00f54ff",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 08:20:14 UTC",
    "User": "root"
  },
  "Author": "Martin Morgan [aut],\nSean Davis [aut, cre],\nMarcel Ramos [ctb]",
  "Maintainer": "Sean Davis <seandavi@gmail.com>",
  "MD5sum": "7ea498a9cff7e6681c19a626b94588cf",
  "_user": "bioc",
  "_type": "src",
  "_file": "GenomicDataCommons_1.37.0.tar.gz",
  "_fileid": "7a7cb5400d926a5d30870b790222db8055e979bb7382227d498fa6fa74e097bd",
  "_filesize": 1829076,
  "_sha256": "7a7cb5400d926a5d30870b790222db8055e979bb7382227d498fa6fa74e097bd",
  "_created": "2026-05-30T08:20:14.000Z",
  "_published": "2026-05-30T11:57:13.723Z",
  "_jobs": [
    {
      "job": 78636189179,
      "time": 189,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306800495"
    },
    {
      "job": 78636189182,
      "time": 287,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306809708"
    },
    {
      "job": 78636189191,
      "time": 313,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306812334"
    },
    {
      "job": 78636189190,
      "time": 152,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7307982225"
    },
    {
      "job": 78636189189,
      "time": 332,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307997479"
    },
    {
      "job": 78635899211,
      "time": 339,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306781198"
    },
    {
      "job": 78636189178,
      "time": 187,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306800198"
    },
    {
      "job": 78636189196,
      "time": 210,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306802446"
    },
    {
      "job": 78636189210,
      "time": 186,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7306800139"
    },
    {
      "job": 78636189197,
      "time": 249,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306806089"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 15
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678977562",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/GenomicDataCommons",
  "_commit": {
    "id": "1f1dd57f36ddcd76f4b53c80e81ae993c00f54ff",
    "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": 1777380325
  },
  "_maintainer": {
    "name": "Sean Davis",
    "email": "seandavi@gmail.com",
    "login": "seandavi",
    "description": "Software developer, Pediatric oncologist, Cancer researcher, Data scientist and engineer, Community organizer",
    "uuid": 92435
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "httr",
      "role": "Imports"
    },
    {
      "package": "xml2",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "rappdirs",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "DT",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "listviewer",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "GenomicAlignments",
      "role": "Suggests"
    },
    {
      "package": "Rsamtools",
      "role": "Suggests"
    },
    {
      "package": "BiocParallel",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg38.knownGene",
      "role": "Suggests"
    },
    {
      "package": "VariantAnnotation",
      "role": "Suggests"
    },
    {
      "package": "maftools",
      "role": "Suggests"
    },
    {
      "package": "R.utils",
      "role": "Suggests"
    },
    {
      "package": "data.table",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 13,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2025-45",
      "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": [
    "dataimport",
    "sequencing",
    "api-client",
    "bioconductor",
    "bioinformatics",
    "cancer",
    "core-services",
    "data-science",
    "genomics",
    "nci",
    "tcga",
    "vignette"
  ],
  "_stars": 90,
  "_contributors": [
    {
      "user": "seandavi",
      "count": 430,
      "uuid": 92435
    },
    {
      "user": "mtmorgan",
      "count": 48,
      "uuid": 118552
    },
    {
      "user": "link-ny",
      "count": 21,
      "uuid": 4392950
    },
    {
      "user": "nturaga",
      "count": 19,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 16,
      "uuid": 1744257
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 2137,
    "source": "https://www.bioconductor.org/packages/stats/bioc/GenomicDataCommons"
  },
  "_mentions": 8,
  "_devurl": "https://github.com/bioconductor/genomicdatacommons",
  "_pkgdown": "http://bioconductor.github.io/GenomicDataCommons/",
  "_searchresults": 259,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/GenomicDataCommons.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/bioconductor/genomicdatacommons",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "aggregations",
    "annotations",
    "available_expand",
    "available_fields",
    "available_values",
    "cases",
    "cnv_occurrences",
    "cnvs",
    "count",
    "default_fields",
    "endpoints",
    "entity_name",
    "expand",
    "facet",
    "field_description",
    "files",
    "filter",
    "gdc_cache",
    "gdc_client",
    "gdc_client_version_validate",
    "gdc_clinical",
    "gdc_set_cache",
    "gdc_token",
    "gdcdata",
    "genes",
    "get_facets",
    "get_filter",
    "grep_fields",
    "id_field",
    "ids",
    "make_filter",
    "manifest",
    "mapping",
    "parameters",
    "projects",
    "query",
    "readDNAcopy",
    "readHTSeqFile",
    "response",
    "response_all",
    "results",
    "results_all",
    "select",
    "slicing",
    "ssm_occurrences",
    "ssms",
    "status",
    "transfer",
    "transfer_help",
    "write_manifest"
  ],
  "_help": [
    {
      "page": "GenomicDataCommons-package",
      "title": "GenomicDataCommons: A package for interfacing with the NCI GDC",
      "topics": [
        "GenomicDataCommons-package",
        "GenomicDataCommons"
      ]
    },
    {
      "page": "aggregations",
      "title": "aggregations",
      "topics": [
        "aggregations",
        "aggregations.GDCQuery",
        "aggregations.GDCResponse"
      ]
    },
    {
      "page": "available_expand",
      "title": "Return valid values for \"expand\"",
      "topics": [
        "available_expand",
        "available_expand.character",
        "available_expand.GDCQuery"
      ]
    },
    {
      "page": "available_fields",
      "title": "S3 Generic to return all GDC fields",
      "topics": [
        "available_fields",
        "available_fields.character",
        "available_fields.GDCQuery"
      ]
    },
    {
      "page": "available_values",
      "title": "Find common values for a GDC field",
      "topics": [
        "available_values"
      ]
    },
    {
      "page": "count",
      "title": "provide count of records in a 'GDCQuery'",
      "topics": [
        "count",
        "count.GDCQuery",
        "count.GDCResponse"
      ]
    },
    {
      "page": "default_fields",
      "title": "S3 Generic to return default GDC fields",
      "topics": [
        "default_fields",
        "default_fields.character",
        "default_fields.GDCQuery"
      ]
    },
    {
      "page": "entity_name",
      "title": "Get the entity name from a GDCQuery object",
      "topics": [
        "entity_name",
        "entity_name.GDCQuery",
        "entity_name.GDCResults"
      ]
    },
    {
      "page": "expand",
      "title": "Set the 'expand' parameter",
      "topics": [
        "expand",
        "expand.GDCQuery"
      ]
    },
    {
      "page": "faceting",
      "title": "Set facets for a 'GDCQuery'",
      "topics": [
        "facet",
        "get_facets",
        "get_facets.GDCQuery"
      ]
    },
    {
      "page": "field_description",
      "title": "S3 Generic that returns the field description text, if available",
      "topics": [
        "field_description",
        "field_description.character",
        "field_description.GDCQuery"
      ]
    },
    {
      "page": "filtering",
      "title": "Manipulating GDCQuery filters",
      "topics": [
        "filter",
        "filter.GDCQuery",
        "filtering",
        "get_filter",
        "get_filter.GDCQuery"
      ]
    },
    {
      "page": "gdc_cache",
      "title": "Work with gdc cache directory",
      "topics": [
        "gdc_cache",
        "gdc_set_cache"
      ]
    },
    {
      "page": "gdc_client",
      "title": "return gdc-client executable path",
      "topics": [
        "gdc_client"
      ]
    },
    {
      "page": "gdc_clinical",
      "title": "Get clinical information from GDC",
      "topics": [
        "gdc_clinical"
      ]
    },
    {
      "page": "gdc_token",
      "title": "return a gdc token from file or environment",
      "topics": [
        "gdc_token"
      ]
    },
    {
      "page": "gdcdata",
      "title": "Download GDC files",
      "topics": [
        "gdcdata"
      ]
    },
    {
      "page": "grep_fields",
      "title": "Find matching field names",
      "topics": [
        "grep_fields"
      ]
    },
    {
      "page": "id_field",
      "title": "get the name of the id field",
      "topics": [
        "id_field",
        "id_field.GDCQuery",
        "id_field.GDCResults"
      ]
    },
    {
      "page": "ids",
      "title": "Get the ids associated with a GDC query or response",
      "topics": [
        "ids",
        "ids.GDCManifest",
        "ids.GDCQuery",
        "ids.GDCResponse",
        "ids.GDCResults"
      ]
    },
    {
      "page": "make_filter",
      "title": "Create NCI GDC filters for limiting GDC query results",
      "topics": [
        "make_filter"
      ]
    },
    {
      "page": "manifest",
      "title": "Prepare GDC manifest file for bulk download",
      "topics": [
        "manifest",
        "manifest.GDCcasesResponse",
        "manifest.GDCfilesResponse",
        "manifest.gdc_files"
      ]
    },
    {
      "page": "mapping",
      "title": "Query GDC for available endpoint fields",
      "topics": [
        "mapping"
      ]
    },
    {
      "page": "query",
      "title": "Start a query of GDC metadata",
      "topics": [
        "annotations",
        "cases",
        "cnvs",
        "cnv_occurrences",
        "files",
        "GDCQuery",
        "genes",
        "projects",
        "query",
        "ssms",
        "ssm_occurrences"
      ]
    },
    {
      "page": "readDNAcopy",
      "title": "Read DNAcopy results into GRanges object",
      "topics": [
        "readDNAcopy"
      ]
    },
    {
      "page": "readHTSeqFile",
      "title": "Read a single htseq-counts result file.",
      "topics": [
        "readHTSeqFile"
      ]
    },
    {
      "page": "response",
      "title": "Fetch 'GDCQuery' metadata from GDC",
      "topics": [
        "GDCResponse",
        "response",
        "response.GDCQuery",
        "response_all"
      ]
    },
    {
      "page": "results",
      "title": "results",
      "topics": [
        "results",
        "results.GDCQuery",
        "results.GDCResponse"
      ]
    },
    {
      "page": "results_all",
      "title": "results_all",
      "topics": [
        "results_all",
        "results_all.GDCQuery",
        "results_all.GDCResponse"
      ]
    },
    {
      "page": "select",
      "title": "S3 generic to set GDCQuery fields",
      "topics": [
        "select",
        "select.GDCQuery"
      ]
    },
    {
      "page": "slicing",
      "title": "Query GDC for data slices",
      "topics": [
        "slicing"
      ]
    },
    {
      "page": "status",
      "title": "Query the GDC for current status",
      "topics": [
        "status"
      ]
    },
    {
      "page": "transfer",
      "title": "Bulk data download",
      "topics": [
        "gdc_client_version_validate",
        "transfer",
        "transfer_help"
      ]
    },
    {
      "page": "write_manifest",
      "title": "write a manifest data.frame to disk",
      "topics": [
        "write_manifest"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/GenomicDataCommons/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "BiocGenerics",
    "bit",
    "bit64",
    "cli",
    "clipr",
    "cpp11",
    "crayon",
    "curl",
    "dplyr",
    "generics",
    "GenomicRanges",
    "glue",
    "hms",
    "httr",
    "IRanges",
    "jsonlite",
    "lifecycle",
    "magrittr",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "readr",
    "rlang",
    "S4Vectors",
    "Seqinfo",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "vroom",
    "withr",
    "xml2"
  ],
  "_vignettes": [
    {
      "source": "overview.Rmd",
      "filename": "overview.html",
      "title": "The GenomicDataCommons Package",
      "author": "Sean Davis & Martin Morgan",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What is the GDC?",
        "Quickstart",
        "Installation",
        "Check connectivity and status",
        "Find data",
        "Download data",
        "Metadata queries",
        "Clinical data",
        "General metadata queries",
        "Basic design",
        "Usage",
        "Querying metadata",
        "Creating a query",
        "Retrieving results",
        "Fields and Values",
        "Facets and aggregation",
        "Filtering",
        "Authentication",
        "Datafile access and download",
        "Data downloads via the GDC API",
        "Bulk downloads",
        "BAM slicing",
        "Use Cases",
        "Cases",
        "How many cases are there per project_id?",
        "How many cases are included in all TARGET projects?",
        "How many cases are included in all TCGA projects?",
        "What is the breakdown of sample types in TCGA-BRCA?",
        "Fetch all samples in TCGA-BRCA that use \"Solid Tissue\" as a normal.",
        "Get all TCGA case ids that are female",
        "Get all TCGA-COAD case ids that are NOT female",
        "Get all TCGA cases that are missing gender",
        "Get all TCGA cases that are NOT missing gender",
        "Files",
        "How many of each type of file are available?",
        "Find gene-level RNA-seq quantification files for GBM",
        "Slicing",
        "Get all BAM file ids from TCGA-GBM",
        "Troubleshooting",
        "SSL connection errors",
        "sessionInfo()",
        "Developer notes"
      ],
      "created": "2016-06-20 21:28:06",
      "modified": "2024-05-06 20:42:37",
      "commits": 63
    },
    {
      "source": "questions-and-answers.Rmd",
      "filename": "questions-and-answers.html",
      "title": "Questions and answers from over the years",
      "author": "Sean Davis",
      "engine": "knitr::rmarkdown",
      "headings": [
        "How could I generate a manifest file with filtering of Race and Ethnicity?",
        "How can I get the number of cases with RNA-Seq data added by date to TCGA project with GenomicDataCommons?"
      ],
      "created": "2021-08-09 19:16:48",
      "modified": "2024-05-15 21:04:26",
      "commits": 3
    },
    {
      "source": "somatic_mutations.Rmd",
      "filename": "somatic_mutations.html",
      "title": "Working with simple somatic mutations",
      "author": "Sean Davis",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Background",
        "Workflow",
        "Genes and gene details",
        "ssms",
        "convert to VRanges",
        "OncoPrint"
      ],
      "created": "2020-01-28 02:33:10",
      "modified": "2024-05-06 20:42:37",
      "commits": 8
    }
  ],
  "_score": 11.622865153862076,
  "_indexed": true,
  "_nocasepkg": "genomicdatacommons",
  "_universes": [
    "bioc",
    "seandavi",
    "bioconductor"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.37.0",
      "date": "2026-05-30T08:24:26.000Z",
      "distro": "noble",
      "commit": "1f1dd57f36ddcd76f4b53c80e81ae993c00f54ff",
      "fileid": "20bcf62ad22eccb8726c11437a28f17a572ab2b53be2a3b818fff74f033fe7c8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678977562"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.37.0",
      "date": "2026-05-30T08:24:41.000Z",
      "distro": "noble",
      "commit": "1f1dd57f36ddcd76f4b53c80e81ae993c00f54ff",
      "fileid": "1f79919ad5631df947c33a050cdc5833a53f2d80f292382b8a4ab2fb5a747027",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678977562"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.37.0",
      "date": "2026-05-30T11:53:00.000Z",
      "commit": "1f1dd57f36ddcd76f4b53c80e81ae993c00f54ff",
      "fileid": "9f599e4b77d0c9004a4629575d6f076c70a57e7c9428f38222fc5bcd4f4fc8ce",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678977562"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.37.0",
      "date": "2026-05-30T11:56:01.000Z",
      "commit": "1f1dd57f36ddcd76f4b53c80e81ae993c00f54ff",
      "fileid": "c5fbc9ab819fa70d03a12b648462a5fe237b347638106f95d84ea6b35c36f8d2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678977562"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.37.0",
      "date": "2026-05-30T08:23:43.000Z",
      "commit": "1f1dd57f36ddcd76f4b53c80e81ae993c00f54ff",
      "fileid": "d3d0e75b8b001957a664a29adb271dd9daccf17e88e954b2563f072dddef5d19",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678977562"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-05-30T08:22:49.000Z",
      "commit": "1f1dd57f36ddcd76f4b53c80e81ae993c00f54ff",
      "fileid": "0c07fb0a69909d0ae83238efe68fa9cc0eae63ea791e8edfc747c5097ed90a19",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678977562"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-05-30T08:22:29.000Z",
      "commit": "1f1dd57f36ddcd76f4b53c80e81ae993c00f54ff",
      "fileid": "1c3d30b3122d200a615ec160ecadbca2551699db7927c2ee553644941c5559ca",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678977562"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-05-30T08:22:43.000Z",
      "commit": "1f1dd57f36ddcd76f4b53c80e81ae993c00f54ff",
      "fileid": "f44b4a3805c5abc47eedce1af7c7d0dd7f7468b0722809db40e8448c9e1bf293",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678977562"
    }
  ]
}