{
  "_id": "6a101ac9acfb0bcc41c86aff",
  "Package": "TCGAbiolinks",
  "Type": "Package",
  "Title": "TCGAbiolinks: An R/Bioconductor package for integrative analysis\nwith GDC data",
  "Version": "2.41.0",
  "Date": "2024-01-01",
  "Author": "Antonio Colaprico, Tiago Chedraoui Silva, Catharina Olsen,\nLuciano Garofano, Davide Garolini, Claudia Cava, Thais Sabedot,\nTathiane Malta, Stefano M. Pagnotta, Isabella Castiglioni,\nMichele Ceccarelli, Gianluca Bontempi, Houtan Noushmehr",
  "Maintainer": "Tiago Chedraoui Silva <tiagochst@gmail.com>, Antonio\nColaprico <axc1833@med.miami.edu>",
  "Description": "The aim of TCGAbiolinks is : i) facilitate the GDC\nopen-access data retrieval, ii) prepare the data using the\nappropriate pre-processing strategies, iii) provide the means\nto carry out different standard analyses and iv) to easily\nreproduce earlier research results. In more detail, the package\nprovides multiple methods for analysis (e.g., differential\nexpression analysis, identifying differentially methylated\nregions) and methods for visualization (e.g., survival plots,\nvolcano plots, starburst plots) in order to easily develop\ncomplete analysis pipelines.",
  "License": "GPL (>= 3)",
  "biocViews": "DNAMethylation, DifferentialMethylation, GeneRegulation,\nGeneExpression, MethylationArray, DifferentialExpression,\nPathways, Network, Sequencing, Survival, Software",
  "VignetteBuilder": "knitr",
  "LazyData": "true",
  "URL": "https://github.com/BioinformaticsFMRP/TCGAbiolinks",
  "BugReports": "https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues",
  "RoxygenNote": "7.3.3",
  "Encoding": "UTF-8",
  "Config/pak/sysreqs": "libicu-dev libpng-dev libxml2-dev libssl-dev\nlibx11-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:41:41 UTC",
  "RemoteUrl": "https://github.com/bioc/TCGAbiolinks",
  "RemoteRef": "HEAD",
  "RemoteSha": "33002fe2c07eeb73ac4b76b844e86d3cb7a0adde",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-14 09:51:25 UTC",
    "User": "root"
  },
  "MD5sum": "e9a56199cdd42f862483e1c0a03ac5fa",
  "_user": "bioc",
  "_type": "src",
  "_file": "TCGAbiolinks_2.41.0.tar.gz",
  "_fileid": "e23d96863e07cada1bf069c6833b13a342ed8c343d2a2d93b26b7f40ab01ed7b",
  "_filesize": 31936294,
  "_sha256": "e23d96863e07cada1bf069c6833b13a342ed8c343d2a2d93b26b7f40ab01ed7b",
  "_created": "2026-05-14T09:51:25.000Z",
  "_published": "2026-05-22T08:58:49.404Z",
  "_jobs": [
    {
      "job": 77347725618,
      "time": 403,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "6991835595"
    },
    {
      "job": 77347725761,
      "time": 769,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "6991936089"
    },
    {
      "job": 77347726004,
      "time": 795,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "6991943394"
    },
    {
      "job": 77347725660,
      "time": 642,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "6991898486"
    },
    {
      "job": 77347725773,
      "time": 558,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "6991877428"
    },
    {
      "job": 77347725390,
      "time": 640,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6991716137"
    },
    {
      "job": 77347725238,
      "time": 306,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7156699110"
    },
    {
      "job": 77347725625,
      "time": 653,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "6991903509"
    },
    {
      "job": 77347725870,
      "time": 804,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "6991946675"
    },
    {
      "job": 77347726124,
      "time": 668,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "6991907492"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 2,
    "note": 21
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25853160116",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/TCGAbiolinks",
  "_commit": {
    "id": "33002fe2c07eeb73ac4b76b844e86d3cb7a0adde",
    "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": 1777380101
  },
  "_maintainer": {
    "name": "Tiago Chedraoui Silva",
    "email": "axc1833@med.miami.edu",
    "login": "tiagochst",
    "uuid": 145529
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "downloader",
      "version": ">= 0.4",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "biomaRt",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "XML",
      "version": ">= 3.98.0",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "version": ">= 1.0.0",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "version": ">= 1.0.0",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "rvest",
      "version": ">= 0.3.0",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "R.utils",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "version": ">= 1.4.0",
      "role": "Imports"
    },
    {
      "package": "TCGAbiolinksGUI.data",
      "version": ">= 1.15.1",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "xml2",
      "role": "Imports"
    },
    {
      "package": "httr",
      "version": ">= 1.2.1",
      "role": "Imports"
    },
    {
      "package": "jpeg",
      "role": "Suggests"
    },
    {
      "package": "png",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    },
    {
      "package": "maftools",
      "role": "Suggests"
    },
    {
      "package": "parmigene",
      "role": "Suggests"
    },
    {
      "package": "c3net",
      "role": "Suggests"
    },
    {
      "package": "minet",
      "role": "Suggests"
    },
    {
      "package": "Biobase",
      "role": "Suggests"
    },
    {
      "package": "affy",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "sesame",
      "role": "Suggests"
    },
    {
      "package": "AnnotationHub",
      "role": "Suggests"
    },
    {
      "package": "ExperimentHub",
      "role": "Suggests"
    },
    {
      "package": "pathview",
      "role": "Suggests"
    },
    {
      "package": "clusterProfiler",
      "role": "Suggests"
    },
    {
      "package": "Seurat",
      "role": "Suggests"
    },
    {
      "package": "ComplexHeatmap",
      "role": "Suggests"
    },
    {
      "package": "circlize",
      "role": "Suggests"
    },
    {
      "package": "ConsensusClusterPlus",
      "role": "Suggests"
    },
    {
      "package": "igraph",
      "role": "Suggests"
    },
    {
      "package": "limma",
      "role": "Suggests"
    },
    {
      "package": "edgeR",
      "role": "Suggests"
    },
    {
      "package": "sva",
      "role": "Suggests"
    },
    {
      "package": "EDASeq",
      "role": "Suggests"
    },
    {
      "package": "survminer",
      "role": "Suggests"
    },
    {
      "package": "genefilter",
      "role": "Suggests"
    },
    {
      "package": "gridExtra",
      "role": "Suggests"
    },
    {
      "package": "survival",
      "role": "Suggests"
    },
    {
      "package": "doParallel",
      "role": "Suggests"
    },
    {
      "package": "parallel",
      "role": "Suggests"
    },
    {
      "package": "ggrepel",
      "version": ">= 0.6.3",
      "role": "Suggests"
    },
    {
      "package": "scales",
      "role": "Suggests"
    },
    {
      "package": "grid",
      "role": "Suggests"
    },
    {
      "package": "DT",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 7,
  "_updates": [
    {
      "week": "2025-25",
      "n": 3
    },
    {
      "week": "2025-40",
      "n": 2
    },
    {
      "week": "2025-41",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.41.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.40.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "dnamethylation",
    "differentialmethylation",
    "generegulation",
    "geneexpression",
    "methylationarray",
    "differentialexpression",
    "pathways",
    "network",
    "sequencing",
    "survival",
    "software",
    "bioc",
    "bioconductor",
    "gdc",
    "integrative-analysis",
    "tcga",
    "tcga-data",
    "tcgabiolinks"
  ],
  "_stars": 351,
  "_contributors": [
    {
      "user": "tiagochst",
      "count": 21266,
      "uuid": 145529
    },
    {
      "user": "torongs82",
      "count": 2879,
      "uuid": 9592554
    },
    {
      "user": "simomounir",
      "count": 249,
      "uuid": 18674957
    },
    {
      "user": "colsen",
      "count": 76,
      "uuid": 596426
    },
    {
      "user": "melkiades",
      "count": 66,
      "uuid": 11279768
    },
    {
      "user": "vobencha",
      "count": 54,
      "uuid": 2466173
    },
    {
      "user": "nturaga",
      "count": 48,
      "uuid": 2746443
    },
    {
      "user": "lucgar",
      "count": 38,
      "uuid": 9592544
    },
    {
      "user": "dtenenba",
      "count": 36,
      "uuid": 2286826
    },
    {
      "user": "melkaz",
      "count": 27,
      "uuid": 1302218
    },
    {
      "user": "link-ny",
      "count": 27,
      "uuid": 4392950
    },
    {
      "user": "hpages",
      "count": 24,
      "uuid": 8810451
    },
    {
      "user": "romagnolid",
      "count": 22,
      "uuid": 10038298
    },
    {
      "user": "juggernaut93",
      "count": 12,
      "uuid": 8384905
    },
    {
      "user": "jwokaty",
      "count": 12,
      "uuid": 1744257
    },
    {
      "user": "tiagomaie",
      "count": 8,
      "uuid": 8191845
    },
    {
      "user": "nolanbentley",
      "count": 5,
      "uuid": 12236960
    },
    {
      "user": "yue-jiang",
      "count": 4,
      "uuid": 14319630
    },
    {
      "user": "jimhester",
      "count": 3,
      "uuid": 205275
    },
    {
      "user": "warbol",
      "count": 2,
      "uuid": 90440697
    },
    {
      "user": "fabianjkrueger",
      "count": 1,
      "uuid": 101988719
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 9080,
    "source": "https://www.bioconductor.org/packages/stats/bioc/TCGAbiolinks"
  },
  "_mentions": 276,
  "_devurl": "https://github.com/bioinformaticsfmrp/tcgabiolinks",
  "_searchresults": 2408,
  "_rbuild": "4.6.0",
  "_assets": [
    "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",
    "extra/TCGAbiolinks.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/bioinformaticsfmrp/tcgabiolinks",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "colDataPrepare",
    "gaiaCNVplot",
    "GDCdownload",
    "GDCprepare",
    "GDCprepare_clinic",
    "GDCquery",
    "GDCquery_ATAC_seq",
    "GDCquery_clinic",
    "get_IDs",
    "get.GRCh.bioMart",
    "getAdjacencyBiogrid",
    "getDataCategorySummary",
    "getGDCInfo",
    "getGDCprojects",
    "getGistic",
    "getLinkedOmicsData",
    "getManifest",
    "getMC3MAF",
    "getProjectSummary",
    "getResults",
    "getSampleFilesSummary",
    "gliomaClassifier",
    "isServeOK",
    "matchedMetExp",
    "PanCancerAtlas_subtypes",
    "TCGA_MolecularSubtype",
    "TCGAanalyze_analyseGRN",
    "TCGAanalyze_Clustering",
    "TCGAanalyze_DEA",
    "TCGAanalyze_DEA_Affy",
    "TCGAanalyze_DMC",
    "TCGAanalyze_EAcomplete",
    "TCGAanalyze_Filtering",
    "TCGAanalyze_LevelTab",
    "TCGAanalyze_networkInference",
    "TCGAanalyze_Normalization",
    "TCGAanalyze_Pathview",
    "TCGAanalyze_Preprocessing",
    "TCGAanalyze_Stemness",
    "TCGAanalyze_survival",
    "TCGAanalyze_SurvivalKM",
    "TCGAbatch_Correction",
    "TCGAprepare_Affy",
    "TCGAquery_MatchedCoupledSampleTypes",
    "TCGAquery_recount2",
    "TCGAquery_SampleTypes",
    "TCGAquery_subtype",
    "TCGAtumor_purity",
    "TCGAvisualize_BarPlot",
    "TCGAvisualize_EAbarplot",
    "TCGAvisualize_Heatmap",
    "TCGAvisualize_meanMethylation",
    "TCGAvisualize_oncoprint",
    "TCGAvisualize_PCA",
    "TCGAvisualize_starburst",
    "TCGAVisualize_volcano",
    "UseRaw_afterFilter"
  ],
  "_datasets": [
    {
      "name": "bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf",
      "title": "TCGA CHOL MAF",
      "object": "bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Hugo_Symbol",
        "Entrez_Gene_Id",
        "Center",
        "NCBI_Build",
        "Chromosome",
        "Start_Position",
        "End_Position",
        "Strand",
        "Variant_Classification",
        "Variant_Type",
        "Reference_Allele",
        "Tumor_Seq_Allele1",
        "Tumor_Seq_Allele2",
        "dbSNP_RS",
        "dbSNP_Val_Status",
        "Tumor_Sample_Barcode",
        "Matched_Norm_Sample_Barcode",
        "Match_Norm_Seq_Allele1",
        "Match_Norm_Seq_Allele2",
        "Tumor_Validation_Allele1",
        "Tumor_Validation_Allele2",
        "Match_Norm_Validation_Allele1",
        "Match_Norm_Validation_Allele2",
        "Verification_Status",
        "Validation_Status",
        "Mutation_Status",
        "Sequencing_Phase",
        "Sequence_Source",
        "Validation_Method",
        "Score",
        "BAM_File",
        "Sequencer",
        "Tumor_Sample_UUID",
        "Matched_Norm_Sample_UUID"
      ],
      "rows": 3555,
      "table": true,
      "tojson": true
    },
    {
      "name": "chol_maf",
      "title": "TCGA CHOL MAF transformed to maftools object",
      "object": "chol_maf",
      "class": [
        "MAF"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "clinical.biotab",
      "title": "A list of data frames with clinical data parsed from XML (code in vignettes)",
      "object": "clinical.biotab",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "dataBRCA",
      "title": "TCGA data matrix BRCA",
      "object": "dataBRCA",
      "class": [
        "data.frame"
      ],
      "fields": [
        "TCGA-A7-A13D-01A-13R-A12P-07",
        "TCGA-BH-A0DK-11A-13R-A089-07",
        "TCGA-BH-A1FC-11A-32R-A13Q-07",
        "TCGA-E9-A1RH-11A-34R-A169-07",
        "TCGA-A7-A13G-11A-51R-A13Q-07",
        "TCGA-AQ-A0Y5-01A-11R-A14M-07",
        "TCGA-E9-A1NG-11A-52R-A14M-07",
        "TCGA-A2-A0CV-01A-31R-A115-07",
        "TCGA-C8-A1HJ-01A-11R-A13Q-07",
        "TCGA-BH-A0AU-01A-11R-A12P-07"
      ],
      "rows": 20530,
      "table": true,
      "tojson": true
    },
    {
      "name": "dataDEGsFiltLevel",
      "title": "TCGA data matrix BRCA DEGs",
      "object": "dataDEGsFiltLevel",
      "class": [
        "data.frame"
      ],
      "fields": [
        "mRNA",
        "logFC",
        "FDR",
        "Tumor",
        "Normal",
        "Delta"
      ],
      "rows": 3649,
      "table": true,
      "tojson": true
    },
    {
      "name": "dataREAD",
      "title": "TCGA data SummarizedExperiment READ",
      "object": "dataREAD",
      "class": [
        "RangedSummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "dataREAD_df",
      "title": "TCGA data matrix READ",
      "object": "dataREAD_df",
      "class": [
        "data.frame"
      ],
      "fields": [
        "TCGA-DY-A1DE-01A-11R-A155-07",
        "TCGA-DY-A0XA-01A-11R-A155-07"
      ],
      "rows": 20531,
      "table": true,
      "tojson": true
    },
    {
      "name": "DE_PCBC_stemSig",
      "title": "A numeric vector with SC-derived definitive endoderm (DE) signature trained on PCBC's dataset",
      "object": "DE_PCBC_stemSig",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "EB_PCBC_stemSig",
      "title": "A numeric vector with stem cell (SC)-derived embryoid bodies (EB) signature trained on PCBC's dataset",
      "object": "EB_PCBC_stemSig",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "ECTO_PCBC_stemSig",
      "title": "A numeric vector with SC-derived ectoderm (ECTO) signature trained on PCBC's dataset",
      "object": "ECTO_PCBC_stemSig",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "gbm.exp.harmonized",
      "title": "A RangedSummarizedExperiment two samples with gene expression data from vignette aligned against hg38",
      "object": "gbm.exp.harmonized",
      "class": [
        "RangedSummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "gbm.exp.legacy",
      "title": "A RangedSummarizedExperiment two samples with gene expression data from vignette aligned against hg19",
      "object": "gbm.exp.legacy",
      "class": [
        "RangedSummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "geneInfo",
      "title": "geneInfo for normalization of RNAseq data",
      "object": "geneInfo",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "geneLength",
        "gcContent",
        "chr"
      ],
      "rows": 20531,
      "table": true,
      "tojson": true
    },
    {
      "name": "geneInfoHT",
      "title": "geneInfoHT for normalization of HTseq data",
      "object": "geneInfoHT",
      "class": [
        "data.frame"
      ],
      "fields": [
        "geneLength",
        "gcContent"
      ],
      "rows": 68016,
      "table": true,
      "tojson": true
    },
    {
      "name": "MESO_PCBC_stemSig",
      "title": "A numeric vector with SC-derived mesoderm (MESO) signature trained on PCBC's dataset",
      "object": "MESO_PCBC_stemSig",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "met.gbm.27k",
      "title": "A DNA methylation RangedSummarizedExperiment for 8 samples (only first 20 probes) aligned against hg19",
      "object": "met.gbm.27k",
      "class": [
        "RangedSummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "msi_results",
      "title": "MSI data for two samples",
      "object": "msi_results",
      "class": [
        "data.frame"
      ],
      "fields": [
        "bcr_aliquot_uuid",
        "mononucleotide_and_dinucleotide_marker_panel_analysis_status",
        "mononucleotide_marker_panel_analysis_status",
        "bcr_patient_barcode"
      ],
      "rows": 2,
      "table": true,
      "tojson": true
    },
    {
      "name": "SC_PCBC_stemSig",
      "title": "A numeric vector with stem cell-like signature trained on PCBC's dataset",
      "object": "SC_PCBC_stemSig",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "TabSubtypesCol_merged",
      "title": "TCGA samples with their Pam50 subtypes",
      "object": "TabSubtypesCol_merged",
      "class": [
        "data.frame"
      ],
      "fields": [
        "samples",
        "subtype",
        "color"
      ],
      "rows": 4768,
      "table": true,
      "tojson": true
    },
    {
      "name": "tabSurvKMcompleteDEGs",
      "title": "tabSurvKMcompleteDEGs",
      "object": "tabSurvKMcompleteDEGs",
      "class": [
        "data.frame"
      ],
      "fields": [
        "pvalue",
        "Cancer Deaths",
        "Cancer Deaths with Top",
        "Cancer Deaths with Down",
        "Mean Tumor Top",
        "Mean Tumor Down",
        "Mean Normal"
      ],
      "rows": 200,
      "table": true,
      "tojson": true
    },
    {
      "name": "Tumor.purity",
      "title": "TCGA samples with their Tumor Purity measures",
      "object": "Tumor.purity",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Sample.ID",
        "Cancer.type",
        "ESTIMATE",
        "ABSOLUTE",
        "LUMP",
        "IHC",
        "CPE"
      ],
      "rows": 9364,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "colDataPrepare",
      "title": "Create samples information matrix for GDC samples",
      "topics": [
        "colDataPrepare"
      ]
    },
    {
      "page": "dmc.non.parametric",
      "title": "Perform non-parametrix wilcoxon test",
      "topics": [
        "dmc.non.parametric"
      ]
    },
    {
      "page": "gaiaCNVplot",
      "title": "Creates a plot for GAIA output (all significant aberrant regions.)",
      "topics": [
        "gaiaCNVplot"
      ]
    },
    {
      "page": "GDCdownload",
      "title": "Download GDC data",
      "topics": [
        "GDCdownload"
      ]
    },
    {
      "page": "GDCprepare",
      "title": "Prepare GDC data",
      "topics": [
        "GDCprepare"
      ]
    },
    {
      "page": "GDCprepare_clinic",
      "title": "Parsing clinical xml files",
      "topics": [
        "GDCprepare_clinic"
      ]
    },
    {
      "page": "GDCquery",
      "title": "Query GDC data",
      "topics": [
        "GDCquery"
      ]
    },
    {
      "page": "GDCquery_ATAC_seq",
      "title": "Retrieve open access ATAC-seq files from GDC server",
      "topics": [
        "GDCquery_ATAC_seq"
      ]
    },
    {
      "page": "GDCquery_clinic",
      "title": "Get GDC clinical data",
      "topics": [
        "GDCquery_clinic"
      ]
    },
    {
      "page": "get_IDs",
      "title": "Extract information from TCGA barcodes.",
      "topics": [
        "get_IDs"
      ]
    },
    {
      "page": "get.GRCh.bioMart",
      "title": "Get hg19 gene annotation or hg38 (gencode v36)",
      "topics": [
        "get.GRCh.bioMart"
      ]
    },
    {
      "page": "getAdjacencyBiogrid",
      "title": "Get a matrix of interactions of genes from biogrid",
      "topics": [
        "getAdjacencyBiogrid"
      ]
    },
    {
      "page": "getDataCategorySummary",
      "title": "Create a Summary table for each sample in a project saying if it contains or not files for a certain data category",
      "topics": [
        "getDataCategorySummary"
      ]
    },
    {
      "page": "getGDCInfo",
      "title": "Check GDC server status",
      "topics": [
        "getGDCInfo"
      ]
    },
    {
      "page": "getGDCprojects",
      "title": "Retrieve all GDC projects",
      "topics": [
        "getGDCprojects"
      ]
    },
    {
      "page": "getGistic",
      "title": "Download GISTIC data from firehose",
      "topics": [
        "getGistic"
      ]
    },
    {
      "page": "getLinkedOmicsData",
      "title": "Retrieve linkedOmics data",
      "topics": [
        "getLinkedOmicsData"
      ]
    },
    {
      "page": "getManifest",
      "title": "Get a Manifest from GDCquery output that can be used with GDC-client",
      "topics": [
        "getManifest"
      ]
    },
    {
      "page": "getMC3MAF",
      "title": "Retrieve open access mc3 MAF file from GDC server",
      "topics": [
        "getMC3MAF"
      ]
    },
    {
      "page": "getNbCases",
      "title": "Get Number of cases in GDC for a project",
      "topics": [
        "getNbCases"
      ]
    },
    {
      "page": "getNbFiles",
      "title": "Get Number of files in GDC for a project",
      "topics": [
        "getNbFiles"
      ]
    },
    {
      "page": "getProjectSummary",
      "title": "Get Project Summary from GDC",
      "topics": [
        "getProjectSummary"
      ]
    },
    {
      "page": "getResults",
      "title": "Get the results table from query",
      "topics": [
        "getResults"
      ]
    },
    {
      "page": "getSampleFilesSummary",
      "title": "Retrieve summary of files per sample in a project",
      "topics": [
        "getSampleFilesSummary"
      ]
    },
    {
      "page": "getTSS",
      "title": "getTSS to fetch GENCODE gene annotation (transcripts level) from Bioconductor package biomaRt If upstream and downstream are specified in TSS list, promoter regions of GENCODE gene will be generated.",
      "topics": [
        "getTSS"
      ]
    },
    {
      "page": "gliomaClassifier",
      "title": "Gliomar classifier",
      "topics": [
        "gliomaClassifier"
      ]
    },
    {
      "page": "isServeOK",
      "title": "Check GDC server status is OK",
      "topics": [
        "isServeOK"
      ]
    },
    {
      "page": "matchedMetExp",
      "title": "Get GDC primary tumors samples with both DNA methylation (HM450K) and Gene expression data",
      "topics": [
        "matchedMetExp"
      ]
    },
    {
      "page": "PanCancerAtlas_subtypes",
      "title": "Retrieve table with TCGA molecular subtypes",
      "topics": [
        "PanCancerAtlas_subtypes"
      ]
    },
    {
      "page": "splitAPICall",
      "title": "internal function to break a huge API call into smaller ones so it repects the max character limit of a string",
      "topics": [
        "splitAPICall"
      ]
    },
    {
      "page": "TabSubtypesCol_merged",
      "title": "TCGA samples with their Pam50 subtypes",
      "topics": [
        "TabSubtypesCol_merged"
      ]
    },
    {
      "page": "TCGA_MolecularSubtype",
      "title": "Retrieve molecular subtypes for given TCGA barcodes",
      "topics": [
        "TCGA_MolecularSubtype"
      ]
    },
    {
      "page": "TCGAanalyze_analyseGRN",
      "title": "Generate network",
      "topics": [
        "TCGAanalyze_analyseGRN"
      ]
    },
    {
      "page": "TCGAanalyze_Clustering",
      "title": "Hierarchical cluster analysis",
      "topics": [
        "TCGAanalyze_Clustering"
      ]
    },
    {
      "page": "TCGAanalyze_DEA",
      "title": "Differential expression analysis (DEA) using edgeR or limma package.",
      "topics": [
        "TCGAanalyze_DEA"
      ]
    },
    {
      "page": "TCGAanalyze_DEA_Affy",
      "title": "Differentially expression analysis (DEA) using limma package.",
      "topics": [
        "TCGAanalyze_DEA_Affy"
      ]
    },
    {
      "page": "TCGAanalyze_DMC",
      "title": "Differentially methylated regions Analysis",
      "topics": [
        "TCGAanalyze_DMC"
      ]
    },
    {
      "page": "TCGAanalyze_EA",
      "title": "Enrichment analysis of a gene-set with GO [BP,MF,CC] and pathways.",
      "topics": [
        "TCGAanalyze_EA"
      ]
    },
    {
      "page": "TCGAanalyze_EAcomplete",
      "title": "Enrichment analysis for Gene Ontology (GO) [BP,MF,CC] and Pathways",
      "topics": [
        "TCGAanalyze_EAcomplete"
      ]
    },
    {
      "page": "TCGAanalyze_Filtering",
      "title": "Filtering mRNA transcripts and miRNA selecting a threshold.",
      "topics": [
        "TCGAanalyze_Filtering"
      ]
    },
    {
      "page": "TCGAanalyze_LevelTab",
      "title": "Adding information related to DEGs genes from DEA as mean values in two conditions.",
      "topics": [
        "TCGAanalyze_LevelTab"
      ]
    },
    {
      "page": "TCGAanalyze_networkInference",
      "title": "infer gene regulatory networks",
      "topics": [
        "TCGAanalyze_networkInference"
      ]
    },
    {
      "page": "TCGAanalyze_Normalization",
      "title": "normalization mRNA transcripts and miRNA using EDASeq package.",
      "topics": [
        "TCGAanalyze_Normalization"
      ]
    },
    {
      "page": "TCGAanalyze_Pathview",
      "title": "Generate pathview graph",
      "topics": [
        "TCGAanalyze_Pathview"
      ]
    },
    {
      "page": "TCGAanalyze_Preprocessing",
      "title": "Array Array Intensity correlation (AAIC) and correlation boxplot to define outlier",
      "topics": [
        "TCGAanalyze_Preprocessing"
      ]
    },
    {
      "page": "TCGAanalyze_Stemness",
      "title": "Generate Stemness Score based on RNASeq (mRNAsi stemness index) Malta et al., Cell, 2018",
      "topics": [
        "TCGAanalyze_Stemness"
      ]
    },
    {
      "page": "TCGAanalyze_survival",
      "title": "Creates survival analysis",
      "topics": [
        "TCGAanalyze_survival"
      ]
    },
    {
      "page": "TCGAanalyze_SurvivalKM",
      "title": "survival analysis (SA) univariate with Kaplan-Meier (KM) method.",
      "topics": [
        "TCGAanalyze_SurvivalKM"
      ]
    },
    {
      "page": "TCGAbatch_Correction",
      "title": "Batch correction using ComBat and Voom transformation using limma package.",
      "topics": [
        "TCGAbatch_Correction"
      ]
    },
    {
      "page": "TCGAprepare_Affy",
      "title": "Prepare CEL files into an AffyBatch.",
      "topics": [
        "TCGAprepare_Affy"
      ]
    },
    {
      "page": "TCGAquery_MatchedCoupledSampleTypes",
      "title": "Retrieve multiple tissue types from the same patients.",
      "topics": [
        "TCGAquery_MatchedCoupledSampleTypes"
      ]
    },
    {
      "page": "TCGAquery_recount2",
      "title": "Query gene counts of TCGA and GTEx data from the Recount2 project",
      "topics": [
        "TCGAquery_recount2"
      ]
    },
    {
      "page": "TCGAquery_SampleTypes",
      "title": "Retrieve multiple tissue types not from the same patients.",
      "topics": [
        "TCGAquery_SampleTypes"
      ]
    },
    {
      "page": "TCGAquery_subtype",
      "title": "Retrieve molecular subtypes for a given tumor",
      "topics": [
        "TCGAquery_subtype"
      ]
    },
    {
      "page": "TCGAtumor_purity",
      "title": "Filters TCGA barcodes according to purity parameters",
      "topics": [
        "TCGAtumor_purity"
      ]
    },
    {
      "page": "TCGAvisualize_BarPlot",
      "title": "Barplot of subtypes and clinical info in groups of gene expression clustered.",
      "topics": [
        "TCGAvisualize_BarPlot"
      ]
    },
    {
      "page": "TCGAvisualize_EAbarplot",
      "title": "barPlot for a complete Enrichment Analysis",
      "topics": [
        "TCGAvisualize_EAbarplot"
      ]
    },
    {
      "page": "TCGAvisualize_Heatmap",
      "title": "Heatmap with more sensible behavior using heatmap.plus",
      "topics": [
        "TCGAvisualize_Heatmap"
      ]
    },
    {
      "page": "TCGAvisualize_meanMethylation",
      "title": "Mean methylation boxplot",
      "topics": [
        "TCGAvisualize_meanMethylation"
      ]
    },
    {
      "page": "TCGAvisualize_oncoprint",
      "title": "Creating a oncoprint",
      "topics": [
        "TCGAvisualize_oncoprint"
      ]
    },
    {
      "page": "TCGAvisualize_PCA",
      "title": "Principal components analysis (PCA) plot",
      "topics": [
        "TCGAvisualize_PCA"
      ]
    },
    {
      "page": "TCGAvisualize_starburst",
      "title": "Create starburst plot",
      "topics": [
        "TCGAvisualize_starburst"
      ]
    },
    {
      "page": "TCGAvisualize_SurvivalCoxNET",
      "title": "Survival analysis with univariate Cox regression package (dnet)",
      "topics": [
        "TCGAvisualize_SurvivalCoxNET"
      ]
    },
    {
      "page": "TCGAVisualize_volcano",
      "title": "Creates a volcano plot for DNA methylation or gene expression",
      "topics": [
        "TCGAVisualize_volcano"
      ]
    },
    {
      "page": "Tumor.purity",
      "title": "TCGA samples with their Tumor Purity measures",
      "topics": [
        "Tumor.purity"
      ]
    },
    {
      "page": "UseRaw_afterFilter",
      "title": "Use raw count from the DataPrep object which genes are removed by normalization and filtering steps.",
      "topics": [
        "UseRaw_afterFilter"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/TCGAbiolinks/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "askpass",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "biomaRt",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "clipr",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "digest",
    "downloader",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "highr",
    "hms",
    "httr",
    "httr2",
    "IRanges",
    "isoband",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "prettyunits",
    "progress",
    "purrr",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "readr",
    "rlang",
    "RSQLite",
    "rvest",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "selectr",
    "Seqinfo",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "TCGAbiolinksGUI.data",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "index.Rmd",
      "filename": "index.html",
      "title": "Introduction",
      "engine": "knitr::rmarkdown",
      "headings": [
        "News",
        "Citation",
        "Other useful links",
        "Installation",
        "Question and issues",
        "Required libraries",
        "Session info"
      ],
      "created": "2017-02-06 02:40:05",
      "modified": "2022-04-01 16:10:06",
      "commits": 12
    },
    {
      "source": "extension.Rmd",
      "filename": "extension.html",
      "title": "TCGAbiolinks version bump with new functions",
      "author": "Mohamed Mounir",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Support of Therapeutically Applicable Research To Generate Effective Treatments (TARGET) data:",
        "Querying, downloading, and preparing TARGET data:",
        "Preparing BRCA data for downstream analysis: Differential Expression Analysis",
        "UseRaw_afterFilter: Keep raw counts after filtering",
        "TCGA_MolecularSubtype: Query subtypes for cancer data:",
        "Differential expression analysis with TCGAanalyze_DEA():",
        "Limma pipeline",
        "Customization of contrast using ---contrast.formula--- argument:",
        "TCGAbatch_correction: Handle batch correction and lima-voom transformation",
        "TCGAbatch_correction: working with unpublished datasets",
        "TCGAtumor_purity: Filter TCGA samples according to tumor purity",
        "Download GTEx data available through the Recount2 project:"
      ],
      "created": "2018-01-04 20:36:12",
      "modified": "2019-03-18 17:12:37",
      "commits": 7
    },
    {
      "source": "query.Rmd",
      "filename": "query.html",
      "title": "TCGAbiolinks: Searching GDC database",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Useful information",
        "Searching arguments",
        "project options",
        "sample.type options",
        "Harmonized data options",
        "Harmonized database examples",
        "DNA methylation data: Recurrent tumor samples",
        "Samples with DNA methylation and gene expression data",
        "Raw Sequencing Data: Finding the match between file names and barcode for Controlled data.",
        "Get Manifest file",
        "ATAC-seq data",
        "Summary of available files per patient"
      ],
      "created": "2017-02-06 02:40:05",
      "modified": "2025-01-24 15:29:43",
      "commits": 33
    },
    {
      "source": "download_prepare.Rmd",
      "filename": "download_prepare.html",
      "title": "TCGAbiolinks: Downloading and preparing files for analysis",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Downloading and preparing data for analysis",
        "Arguments",
        "GDCdownload",
        "GDCprepare",
        "Search and download data for two samples from database",
        "GDCprepare: Outputs",
        "Harmonized data",
        "Examples",
        "Harmonized database: data aligned against hg38",
        "Copy Number Variation",
        "Copy Number Segment",
        "Gene Level Copy Number",
        "Allele-specific Copy Number Segment",
        "Masked Copy Number Segment",
        "Transcriptome Profiling",
        "Gene Expression Quantification",
        "miRNA Expression Quantification",
        "Isoform Expression Quantification",
        "DNA methylation",
        "Beta-values",
        "IDAT files",
        "Proteome Profiling",
        "Protein Expression Quantification",
        "Clinical",
        "Simple Nucleotide Variation",
        "Masked Somatic Mutation",
        "Single cell"
      ],
      "created": "2017-02-06 02:40:05",
      "modified": "2023-05-06 15:00:13",
      "commits": 39
    },
    {
      "source": "clinical.Rmd",
      "filename": "clinical.html",
      "title": "TCGAbiolinks: Clinical data",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Useful information",
        "BCR Biotab",
        "Clinical",
        "Biospecimen",
        "Clinical indexed data",
        "XML clinical data",
        "Diagnostic Slide (SVS format)",
        "Filter functions",
        "Other useful code"
      ],
      "created": "2017-02-06 02:40:05",
      "modified": "2023-05-18 14:53:48",
      "commits": 40
    },
    {
      "source": "mutation.Rmd",
      "filename": "mutation.html",
      "title": "TCGAbiolinks: Searching, downloading and visualizing mutation files",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Search and Download",
        "Mutation data (hg38)",
        "Mutation data MC3 file",
        "Visualize the data"
      ],
      "created": "2017-02-06 02:40:05",
      "modified": "2023-05-08 16:53:01",
      "commits": 23
    },
    {
      "source": "classifiers.Rmd",
      "filename": "classifiers.html",
      "title": "Classifiers methods",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Classifying gliomas samples with gliomaClassifier",
        "Data",
        "Function",
        "Results",
        "Comparing results with paper"
      ],
      "created": "2019-11-27 18:14:10",
      "modified": "2023-10-05 16:40:21",
      "commits": 5
    },
    {
      "source": "stemness_score.Rmd",
      "filename": "stemness_score.html",
      "title": "Stemness score",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Calculate stemness score with TCGAanalyze_Stemness",
        "Data",
        "Function",
        "Output"
      ],
      "created": "2022-04-18 03:38:19",
      "modified": "2022-05-13 19:03:22",
      "commits": 3
    },
    {
      "source": "subtypes.Rmd",
      "filename": "subtypes.html",
      "title": "Compilation of TCGA molecular subtypes",
      "engine": "knitr::rmarkdown",
      "headings": [
        "PanCancerAtlas_subtypes: Curated molecular subtypes.",
        "TCGAquery_subtype: Working with molecular subtypes data.",
        "Session Information"
      ],
      "created": "2018-01-05 14:08:24",
      "modified": "2023-05-05 18:08:38",
      "commits": 15
    },
    {
      "source": "analysis.Rmd",
      "filename": "analysis.html",
      "title": "Analyzing and visualizing TCGA data",
      "engine": "knitr::rmarkdown",
      "headings": [
        "TCGAanalyze: Analyze data from TCGA.",
        "TCGAanalyze_Preprocessing: Preprocessing of Gene Expression data (IlluminaHiSeq_RNASeqV2)",
        "TCGAanalyze_DEA & TCGAanalyze_LevelTab: Differential expression analysis (DEA)",
        "HTSeq data: Downstream analysis BRCA",
        "miRNA expression data: Downstream analysis BRCA",
        "TCGAanalyze_EAcomplete & TCGAvisualize_EAbarplot: Enrichment Analysis",
        "TCGAanalyze_survival: Survival Analysis",
        "TCGAanalyze_SurvivalKM: Correlating gene expression and Survival Analysis",
        "TCGAanalyze_DMR: Differentially methylated regions Analysis",
        "TCGAvisualize: Visualize results from analysis functions with TCGA's data.",
        "TCGAvisualize_Heatmap: Create heatmaps with cluster bars",
        "TCGAvisualize_Volcano: Create volcano plot",
        "TCGAvisualize_PCA: Principal Component Analysis plot for differentially expressed genes",
        "TCGAvisualize_meanMethylation: Mean DNA Methylation Analysis",
        "TCGAvisualize_starburst: Integration of gene expression and DNA methylation data",
        "Session Information"
      ],
      "created": "2018-01-05 21:21:07",
      "modified": "2023-05-08 16:53:01",
      "commits": 12
    },
    {
      "source": "casestudy.Rmd",
      "filename": "casestudy.html",
      "title": "Case Studies",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Case study n. 1: Pan Cancer downstream analysis BRCA",
        "Case study n. 2: Pan Cancer downstream analysis LGG",
        "Case study n. 3: Integration of methylation and expression for ACC",
        "Case study n. 4: ELMER pipeline - KIRC",
        "Session Information",
        "References"
      ],
      "created": "2018-01-05 14:08:24",
      "modified": "2022-08-12 16:50:53",
      "commits": 23
    }
  ],
  "_score": 14.94763143180086,
  "_indexed": true,
  "_nocasepkg": "tcgabiolinks",
  "_universes": [
    "bioc",
    "tiagochst",
    "bioinformaticsfmrp"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.41.0",
      "date": "2026-05-14T09:57:21.000Z",
      "distro": "noble",
      "commit": "33002fe2c07eeb73ac4b76b844e86d3cb7a0adde",
      "fileid": "aa57628127ac3eeb3ac79c71e135babf064f84668526c707a83bcbbc2170b3cc",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853160116"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.41.0",
      "date": "2026-05-14T09:57:29.000Z",
      "distro": "noble",
      "commit": "33002fe2c07eeb73ac4b76b844e86d3cb7a0adde",
      "fileid": "f125eb086ba8d3640c95e84613f84aa38e3c893aeedcfca97a20852a12f83fae",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853160116"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.41.0",
      "date": "2026-05-14T09:54:59.000Z",
      "commit": "33002fe2c07eeb73ac4b76b844e86d3cb7a0adde",
      "fileid": "3aad8368f765862739fc9c20ab0640caef1e0bcb604e1d36ecfe1ca72d63a898",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853160116"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.41.0",
      "date": "2026-05-14T09:54:54.000Z",
      "commit": "33002fe2c07eeb73ac4b76b844e86d3cb7a0adde",
      "fileid": "d32f7c96a7537ab8cfe2aed0df3cc98e44cbd629c97622b69e36d9e1cdf1617e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853160116"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.41.0",
      "date": "2026-05-14T09:54:54.000Z",
      "commit": "33002fe2c07eeb73ac4b76b844e86d3cb7a0adde",
      "fileid": "7b6f633bfd48ed0797d9421085ea9479eb1360ff6e0036cc1f8331f3240138f1",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853160116"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.41.0",
      "date": "2026-05-14T09:57:26.000Z",
      "commit": "33002fe2c07eeb73ac4b76b844e86d3cb7a0adde",
      "fileid": "13e9be5b8354ec648b75f222b6895636e152814d5c5a6d125441c9fd006648c7",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853160116"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.41.0",
      "date": "2026-05-14T09:54:54.000Z",
      "commit": "33002fe2c07eeb73ac4b76b844e86d3cb7a0adde",
      "fileid": "2bb27d615cb61a16c53e729be6b137cbd4ef9789e4bdb96fbacd8cc59b79e9e7",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853160116"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.41.0",
      "date": "2026-05-22T08:58:10.000Z",
      "commit": "33002fe2c07eeb73ac4b76b844e86d3cb7a0adde",
      "fileid": "6ea591346e22e15815c8b54683b3e615dde4c61a5ebf9d129eb5a9a093019c9f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853160116"
    }
  ]
}