{
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  "Package": "UCSCXenaTools",
  "Title": "Download and Explore Datasets from UCSC Xena Data Hubs",
  "Version": "1.7.0",
  "Authors@R": "c(person(given = \"Shixiang\",\nfamily = \"Wang\",\nrole = c(\"aut\", \"cre\"),\nemail = \"w_shixiang@163.com\",\ncomment = c(ORCID = \"0000-0001-9855-7357\")),\nperson(given = \"Xue-Song\",\nfamily = \"Liu\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-7736-0077\")),\nperson(given = \"Martin\",\nfamily = \"Morgan\",\nrole = \"ctb\"),\nperson(given = \"Christine\",\nfamily = \"Stawitz\",\nrole = \"rev\",\ncomment = \"Christine reviewed the package for ropensci, see <https://github.com/ropensci/software-review/issues/315>\"),\nperson(given = \"Carl\",\nfamily = \"Ganz\",\nrole = \"rev\",\ncomment = \"Carl reviewed the package for ropensci, see <https://github.com/ropensci/software-review/issues/315>\"))",
  "Maintainer": "Shixiang Wang <w_shixiang@163.com>",
  "Description": "Download and explore datasets from UCSC Xena data hubs,\nwhich are a collection of UCSC-hosted public databases such as\nTCGA, ICGC, TARGET, GTEx, CCLE, and others.  Databases are\nnormalized so they can be combined, linked, filtered, explored\nand downloaded.",
  "License": "GPL-3",
  "URL": "https://docs.ropensci.org/UCSCXenaTools/,\nhttps://github.com/ropensci/UCSCXenaTools",
  "BugReports": "https://github.com/ropensci/UCSCXenaTools/issues",
  "VignetteBuilder": "knitr",
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  "Repository": "https://shixiangwang.r-universe.dev",
  "Date/Publication": "2026-02-06 17:29:57 UTC",
  "RemoteUrl": "https://github.com/ropensci/UCSCXenaTools",
  "RemoteRef": "HEAD",
  "RemoteSha": "82ea9ada186f694ac0c47e95417952c67eeed472",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-04 08:06:46 UTC",
    "User": "root"
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  "Author": "Shixiang Wang [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-9855-7357>),\nXue-Song Liu [aut] (ORCID: <https://orcid.org/0000-0002-7736-0077>),\nMartin Morgan [ctb],\nChristine Stawitz [rev] (Christine reviewed the package for ropensci,\nsee <https://github.com/ropensci/software-review/issues/315>),\nCarl Ganz [rev] (Carl reviewed the package for ropensci, see\n<https://github.com/ropensci/software-review/issues/315>)",
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  "_created": "2026-10-04T08:06:46.000Z",
  "_published": "2026-10-04T08:21:33.430Z",
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  "_tags": [
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      "name": "v1.7.0",
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  "_topics": [
    "api-client",
    "bioinformatics",
    "ccle",
    "downloader",
    "icgc",
    "tcga",
    "toil",
    "treehouse",
    "ucsc",
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  "_assets": [
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    "extra/citation.json",
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    "extra/readme.md",
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  ],
  "_exports": [
    ".XenaHub",
    "%>%",
    "availTCGA",
    "cohorts",
    "datasets",
    "downloadTCGA",
    "fetch",
    "fetch_dataset_identifiers",
    "fetch_dataset_samples",
    "fetch_dense_values",
    "fetch_sparse_values",
    "getTCGAdata",
    "has_probeMap",
    "hosts",
    "samples",
    "showTCGA",
    "to_snake",
    "xena_default_hosts",
    "XenaBrowse",
    "XenaDataUpdate",
    "XenaDownload",
    "XenaFilter",
    "XenaGenerate",
    "XenaHub",
    "XenaPrepare",
    "XenaQuery",
    "XenaQueryProbeMap",
    "XenaScan"
  ],
  "_datasets": [
    {
      "name": "XenaData",
      "title": "Xena Hub Information",
      "object": "XenaData",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "XenaHosts",
        "XenaHostNames",
        "XenaCohorts",
        "XenaDatasets",
        "SampleCount",
        "DataSubtype",
        "Label",
        "Type",
        "AnatomicalOrigin",
        "SampleType",
        "Tags",
        "ProbeMap",
        "LongTitle",
        "Citation",
        "Version",
        "Unit",
        "Platform"
      ],
      "rows": 2314,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "availTCGA",
      "title": "Get or Check TCGA Available ProjectID, DataType and FileType",
      "topics": [
        "availTCGA"
      ]
    },
    {
      "page": "cohorts",
      "title": "Get cohorts of XenaHub object",
      "topics": [
        "cohorts"
      ]
    },
    {
      "page": "datasets",
      "title": "Get datasets of XenaHub object",
      "topics": [
        "datasets"
      ]
    },
    {
      "page": "downloadTCGA",
      "title": "Easily Download TCGA Data by Several Options",
      "topics": [
        "downloadTCGA"
      ]
    },
    {
      "page": "fetch",
      "title": "Fetch Data from UCSC Xena Hosts",
      "topics": [
        "fetch",
        "fetch_dataset_identifiers",
        "fetch_dataset_samples",
        "fetch_dense_values",
        "fetch_sparse_values",
        "has_probeMap"
      ]
    },
    {
      "page": "getTCGAdata",
      "title": "Get TCGA Common Data Sets by Project ID and Property",
      "topics": [
        "getTCGAdata"
      ]
    },
    {
      "page": "hosts",
      "title": "Get hosts of XenaHub object",
      "topics": [
        "hosts"
      ]
    },
    {
      "page": "samples",
      "title": "Get Samples of a XenaHub object according to 'by' and 'how' action arguments",
      "topics": [
        "samples"
      ]
    },
    {
      "page": "showTCGA",
      "title": "Show TCGA data structure by Project ID or ALL",
      "topics": [
        "showTCGA"
      ]
    },
    {
      "page": "to_snake",
      "title": "Convert camel case to snake case",
      "topics": [
        "to_snake"
      ]
    },
    {
      "page": "UCSCXenaTools-dynamic",
      "title": "UCSC Xena Dynamic Objects",
      "topics": [
        ".p_all_cohorts",
        ".p_all_datasets",
        ".p_all_datasets_n",
        ".p_all_field_metadata",
        ".p_cohort_samples",
        ".p_cohort_summary",
        ".p_datasets_null_rows",
        ".p_dataset_fetch",
        ".p_dataset_field",
        ".p_dataset_field_examples",
        ".p_dataset_field_n",
        ".p_dataset_gene_probes_values",
        ".p_dataset_gene_probe_avg",
        ".p_dataset_list",
        ".p_dataset_metadata",
        ".p_dataset_probe_signature",
        ".p_dataset_probe_values",
        ".p_dataset_samples",
        ".p_dataset_samples_ndense_matrix",
        ".p_dataset_sources",
        ".p_dataset_status",
        ".p_feature_list",
        ".p_field_codes",
        ".p_field_metadata",
        ".p_gene_transcripts",
        ".p_match_fields",
        ".p_probemap_list",
        ".p_probe_count",
        ".p_ref_gene_exons",
        ".p_ref_gene_position",
        ".p_ref_gene_range",
        ".p_segmented_data_range",
        ".p_segment_data_examples",
        ".p_sparse_data",
        ".p_sparse_data_examples",
        ".p_sparse_data_match_field",
        ".p_sparse_data_match_field_slow",
        ".p_sparse_data_match_partial_field",
        ".p_sparse_data_range",
        ".p_transcript_expression",
        ".xq_all_cohorts",
        ".xq_all_datasets",
        ".xq_all_datasets_n",
        ".xq_all_field_metadata",
        ".xq_cohort_samples",
        ".xq_cohort_summary",
        ".xq_datasets_null_rows",
        ".xq_dataset_fetch",
        ".xq_dataset_field",
        ".xq_dataset_field_examples",
        ".xq_dataset_field_n",
        ".xq_dataset_gene_probes_values",
        ".xq_dataset_gene_probe_avg",
        ".xq_dataset_list",
        ".xq_dataset_metadata",
        ".xq_dataset_probe_signature",
        ".xq_dataset_probe_values",
        ".xq_dataset_samples",
        ".xq_dataset_samples_ndense_matrix",
        ".xq_dataset_sources",
        ".xq_dataset_status",
        ".xq_feature_list",
        ".xq_field_codes",
        ".xq_field_metadata",
        ".xq_gene_transcripts",
        ".xq_match_fields",
        ".xq_probemap_list",
        ".xq_probe_count",
        ".xq_ref_gene_exons",
        ".xq_ref_gene_position",
        ".xq_ref_gene_range",
        ".xq_segmented_data_range",
        ".xq_segment_data_examples",
        ".xq_sparse_data",
        ".xq_sparse_data_examples",
        ".xq_sparse_data_match_field",
        ".xq_sparse_data_match_field_slow",
        ".xq_sparse_data_match_partial_field",
        ".xq_sparse_data_range",
        ".xq_transcript_expression",
        "UCSCXenaTools-dynamic"
      ]
    },
    {
      "page": "xena_default_hosts",
      "title": "UCSC Xena Default Hosts",
      "topics": [
        "xena_default_hosts"
      ]
    },
    {
      "page": "XenaBrowse",
      "title": "View Info of Dataset or Cohort at UCSC Xena Website Using Web browser",
      "topics": [
        "XenaBrowse"
      ]
    },
    {
      "page": "XenaData",
      "title": "Xena Hub Information",
      "topics": [
        "XenaData"
      ]
    },
    {
      "page": "XenaDataUpdate",
      "title": "Get or Update Newest Data Information of UCSC Xena Data Hubs",
      "topics": [
        "XenaDataUpdate"
      ]
    },
    {
      "page": "XenaDownload",
      "title": "Download Datasets from UCSC Xena Hubs",
      "topics": [
        "XenaDownload"
      ]
    },
    {
      "page": "XenaFilter",
      "title": "Filter a XenaHub Object",
      "topics": [
        "XenaFilter"
      ]
    },
    {
      "page": "XenaGenerate",
      "title": "Generate and Subset a XenaHub Object from 'XenaData'",
      "topics": [
        "XenaGenerate"
      ]
    },
    {
      "page": "XenaHub",
      "title": "Generate a XenaHub Object",
      "topics": [
        "XenaHub"
      ]
    },
    {
      "page": "XenaHub-class",
      "title": "Class XenaHub",
      "topics": [
        ".XenaHub",
        "XenaHub-class"
      ]
    },
    {
      "page": "XenaPrepare",
      "title": "Prepare (Load) Downloaded Datasets to R",
      "topics": [
        "XenaPrepare"
      ]
    },
    {
      "page": "XenaQuery",
      "title": "Query URL of Datasets before Downloading",
      "topics": [
        "XenaQuery"
      ]
    },
    {
      "page": "XenaQueryProbeMap",
      "title": "Query ProbeMap URL of Datasets",
      "topics": [
        "XenaQueryProbeMap"
      ]
    },
    {
      "page": "XenaScan",
      "title": "Scan all rows according to user input by a regular expression",
      "topics": [
        "XenaScan"
      ]
    }
  ],
  "_pkglogo": "https://github.com/ropensci/UCSCXenaTools/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/ropensci/UCSCXenaTools/raw/HEAD/README.md",
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    "bit",
    "bit64",
    "cli",
    "clipr",
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    "crayon",
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    "pillar",
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    "tzdb",
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    "vctrs",
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    "withr"
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  "_vignettes": [
    {
      "source": "USCSXenaTools.Rmd",
      "filename": "USCSXenaTools.html",
      "title": "UCSCXenaTools: an R package for Accessing Genomics Data from UCSC Xena platform, from Cancer Multi-omics to Single-cell RNA-seq",
      "author": "Shixiang Wang ShanghaiTech University",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Data Hub List",
        "Usage",
        "XenaData data.frame",
        "Workflow",
        "Browse datasets",
        "More usages",
        "QA",
        "How to resume file from breakpoint",
        "Citation",
        "Acknowledgments"
      ],
      "created": "2018-08-19 08:56:34",
      "modified": "2025-08-19 10:19:34",
      "commits": 44
    }
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