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  "Package": "cbioportalR",
  "Title": "Browse and Query Clinical and Genomic Data from cBioPortal",
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  "Description": "Provides R users with direct access to genomic and\nclinical data from the 'cBioPortal' web resource via\nuser-friendly functions that wrap 'cBioPortal's' existing API\nendpoints\n<https://www.cbioportal.org/api/swagger-ui/index.html>. Users\ncan browse and query genomic data on mutations, copy number\nalterations and fusions, as well as data on tumor mutational\nburden ('TMB'), microsatellite instability status ('MSI'),\n'FACETS' and select clinical data points (depending on the\nstudy). See <https://www.cbioportal.org/> and Gao et al.,\n(2013) <doi:10.1126/scisignal.2004088> for more information on\nthe cBioPortal web resource.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
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  "Roxygen": "list(markdown = TRUE)",
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  "VignetteBuilder": "knitr",
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  "URL": "https://github.com/karissawhiting/cbioportalR,\nhttps://www.karissawhiting.com/cbioportalR/",
  "BugReports": "https://github.com/karissawhiting/cbioportalR/issues",
  "Language": "en-US",
  "Config/pak/sysreqs": "libicu-dev libssl-dev",
  "Repository": "https://karissawhiting.r-universe.dev",
  "Date/Publication": "2024-11-25 16:42:26 UTC",
  "RemoteUrl": "https://github.com/karissawhiting/cbioportalr",
  "RemoteRef": "HEAD",
  "RemoteSha": "f565f88bc45233dea0a4af6ccf436473f76d5e0e",
  "NeedsCompilation": "no",
  "Packaged": {
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    "User": "root"
  },
  "Author": "Karissa Whiting [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0002-4683-1868>)",
  "Maintainer": "Karissa Whiting <karissa.whiting@gmail.com>",
  "MD5sum": "fcc971eeb1d73d5a8ff72b6426b3448e",
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  "_published": "2026-06-02T15:33:09.973Z",
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    "email": "karissa.whiting@gmail.com",
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  "_updates": [],
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    "name": "karissawhiting"
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/cbioportalR"
  },
  "_devurl": "https://github.com/karissawhiting/cbioportalr",
  "_pkgdown": "https://www.karissawhiting.com/cbioportalR/",
  "_searchresults": 35,
  "_rbuild": "4.6.0",
  "_assets": [
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    "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/karissawhiting/cbioportalr",
  "_realowner": "karissawhiting",
  "_cranurl": true,
  "_releases": [
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      "version": "1.0.0",
      "date": "2022-08-10"
    },
    {
      "version": "1.0.1",
      "date": "2022-08-29"
    },
    {
      "version": "1.1.0",
      "date": "2023-10-05"
    },
    {
      "version": "1.1.1",
      "date": "2024-11-20"
    }
  ],
  "_exports": [
    ".get_clinical_by_list_item",
    ".get_clinical_pat_by_list_item",
    ".get_data_by_sample",
    ".get_data_by_study",
    "%>%",
    "available_clinical_attributes",
    "available_gene_panels",
    "available_patients",
    "available_profiles",
    "available_sample_lists",
    "available_samples",
    "available_studies",
    "cbp_api",
    "get_alias",
    "get_cbioportal_token",
    "get_clinical_by_patient",
    "get_clinical_by_sample",
    "get_clinical_by_study",
    "get_cna_by_sample",
    "get_cna_by_study",
    "get_entrez_id",
    "get_fusions_by_sample",
    "get_fusions_by_study",
    "get_gene_panel",
    "get_genes",
    "get_genetics_by_sample",
    "get_genetics_by_study",
    "get_hugo_symbol",
    "get_mutations_by_sample",
    "get_mutations_by_study",
    "get_panel_by_sample",
    "get_samples_by_patient",
    "get_segments_by_sample",
    "get_segments_by_study",
    "get_structural_variants_by_sample",
    "get_structural_variants_by_study",
    "get_study_info",
    "lookup_id",
    "set_cbioportal_db",
    "test_cbioportal_db"
  ],
  "_datasets": [
    {
      "name": "impact_gene_info",
      "title": "IMPACT Gene Meta Data",
      "object": "impact_gene_info",
      "class": [
        "grouped_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "hugo_symbol",
        "platform_341",
        "platform_410",
        "platform_468",
        "entrez_id",
        "alias"
      ],
      "rows": 470,
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "available_clinical_attributes",
      "title": "Get all available clinical attribute IDs for a study",
      "topics": [
        "available_clinical_attributes"
      ]
    },
    {
      "page": "available_gene_panels",
      "title": "Get Available Gene Panels For a Database",
      "topics": [
        "available_gene_panels"
      ]
    },
    {
      "page": "available_patients",
      "title": "Get All Patient IDs in a Study",
      "topics": [
        "available_patients"
      ]
    },
    {
      "page": "available_profiles",
      "title": "Get Available Genomic Profiles For a Study or Database",
      "topics": [
        "available_profiles"
      ]
    },
    {
      "page": "available_sample_lists",
      "title": "Get All Sample Lists Available For a Study",
      "topics": [
        "available_sample_lists"
      ]
    },
    {
      "page": "available_samples",
      "title": "Get All Sample IDs in a Study",
      "topics": [
        "available_samples"
      ]
    },
    {
      "page": "available_studies",
      "title": "Get Metadata on All Available Studies in a Database",
      "topics": [
        "available_studies"
      ]
    },
    {
      "page": "get_alias",
      "title": "Get Gene Name Alias for a Given Hugo Symbol",
      "topics": [
        "get_alias"
      ]
    },
    {
      "page": "get_cbioportal_token",
      "title": "Get cBioPortal Access Token",
      "topics": [
        "get_cbioportal_token"
      ]
    },
    {
      "page": "get_clinical_by_patient",
      "title": "Get clinical data by attribute, study ID and patient ID",
      "topics": [
        "get_clinical_by_patient"
      ]
    },
    {
      "page": "get_clinical_by_sample",
      "title": "Get clinical data by attribute, study ID and sample ID",
      "topics": [
        "get_clinical_by_sample"
      ]
    },
    {
      "page": "get_clinical_by_study",
      "title": "Get all available clinical data for a specified study",
      "topics": [
        "get_clinical_by_study"
      ]
    },
    {
      "page": "get_cna_by_sample",
      "title": "Get CNA By Sample ID",
      "topics": [
        "get_cna_by_sample"
      ]
    },
    {
      "page": "get_cna_by_study",
      "title": "Get CNA By Study",
      "topics": [
        "get_cna_by_study"
      ]
    },
    {
      "page": "get_entrez_id",
      "title": "Get Entrez Gene ID for a given set of Hugo Symbols",
      "topics": [
        "get_entrez_id"
      ]
    },
    {
      "page": "get_fusions_by_sample",
      "title": "Get Fusions By Sample ID",
      "topics": [
        "get_fusions_by_sample",
        "get_structural_variants_by_sample"
      ]
    },
    {
      "page": "get_fusions_by_study",
      "title": "Get Fusions By Study",
      "topics": [
        "get_fusions_by_study",
        "get_structural_variants_by_study"
      ]
    },
    {
      "page": "get_gene_panel",
      "title": "Retrieve Genes Included For a Specified Panel ID",
      "topics": [
        "get_gene_panel"
      ]
    },
    {
      "page": "get_genes",
      "title": "Get A List of Genes for a Specified Database",
      "topics": [
        "get_genes"
      ]
    },
    {
      "page": "get_genetics_by_sample",
      "title": "Get All Genomic Information By Sample IDs",
      "topics": [
        "get_genetics_by_sample"
      ]
    },
    {
      "page": "get_genetics_by_study",
      "title": "Get All Genomic Information By Study",
      "topics": [
        "get_genetics_by_study"
      ]
    },
    {
      "page": "get_hugo_symbol",
      "title": "Get Hugo Symbol for a given set of Entrez IDs",
      "topics": [
        "get_hugo_symbol"
      ]
    },
    {
      "page": "get_mutations_by_sample",
      "title": "Get Mutations By Sample ID",
      "topics": [
        "get_mutations_by_sample"
      ]
    },
    {
      "page": "get_mutations_by_study",
      "title": "Get Mutations By Study ID",
      "topics": [
        "get_mutations_by_study"
      ]
    },
    {
      "page": "get_panel_by_sample",
      "title": "Get Gene Panel by study ID and sample ID",
      "topics": [
        "get_panel_by_sample"
      ]
    },
    {
      "page": "get_samples_by_patient",
      "title": "Get sample IDs for a given set of patient IDs",
      "topics": [
        "get_samples_by_patient"
      ]
    },
    {
      "page": "get_segments_by_sample",
      "title": "Get Copy Number Segmentation Data By Sample ID",
      "topics": [
        "get_segments_by_sample"
      ]
    },
    {
      "page": "get_segments_by_study",
      "title": "Get Copy Number Segmentation Data By Study",
      "topics": [
        "get_segments_by_study"
      ]
    },
    {
      "page": "get_study_info",
      "title": "Get Metadata on All Available Studies in Database or a Specified Study",
      "topics": [
        "get_study_info"
      ]
    },
    {
      "page": "impact_gene_info",
      "title": "IMPACT Gene Meta Data",
      "topics": [
        "impact_gene_info"
      ]
    },
    {
      "page": "lookup_id",
      "title": "Lookup all available information on what studies a sample ID or patient ID belongs to",
      "topics": [
        "lookup_id"
      ]
    },
    {
      "page": "set_cbioportal_db",
      "title": "Connect to cBioPortal DB",
      "topics": [
        "set_cbioportal_db"
      ]
    },
    {
      "page": "test_cbioportal_db",
      "title": "Test the Database Connection Anytime During your R Session",
      "topics": [
        "test_cbioportal_db"
      ]
    }
  ],
  "_pkglogo": "https://github.com/karissawhiting/cbioportalr/raw/HEAD/man/figures/logo.png",
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    "pillar",
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    "stringr",
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    "tibble",
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  "_vignettes": [
    {
      "source": "internal-structure.Rmd",
      "filename": "internal-structure.html",
      "title": "Internal Structure & Guiding Principles",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Guiding Principles",
        "General Structure"
      ],
      "created": "2022-03-15 21:58:53",
      "modified": "2022-07-14 23:19:31",
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    },
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      "source": "overview-of-workflow.Rmd",
      "filename": "overview-of-workflow.html",
      "title": "Overview of Data Retrieval Workflow",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Setup",
        "Get Study Metadata",
        "Pulling Genomic Data",
        "By Study IDs",
        "By Sample IDs",
        "Limit Results to Specified Genes or Panels",
        "Pulling Clinical Data & Sample Metadata"
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  "_indexed": true,
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  "_universes": [
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