Package: cBioPortalData 2.24.0

Marcel Ramos

cBioPortalData: Exposes and Makes Available Data from the cBioPortal Web Resources

The cBioPortalData R package accesses study datasets from the cBio Cancer Genomics Portal. It accesses the data either from the pre-packaged zip / tar files or from the API interface that was recently implemented by the cBioPortal Data Team. The package can provide data in either tabular format or with MultiAssayExperiment object that uses familiar Bioconductor data representations.

Authors:Levi Waldron [aut], Marcel Ramos [aut, cre], Karim Mezhoud [ctb]

cBioPortalData_2.24.0.tar.gz
cBioPortalData_2.24.0.zip(r-4.7)cBioPortalData_2.24.0.zip(r-4.6)cBioPortalData_2.24.0.zip(r-4.5)
cBioPortalData_2.24.0.tgz(r-4.6-any)cBioPortalData_2.24.0.tgz(r-4.5-any)
cBioPortalData_2.24.0.tar.gz(r-4.7-any)cBioPortalData_2.24.0.tar.gz(r-4.6-any)
cBioPortalData_2.24.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
cBioPortalData/json (API)
NEWS

# Install 'cBioPortalData' in R:
install.packages('cBioPortalData', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/waldronlab/cbioportaldata/issues

On BioConductor:cBioPortalData-2.25.1(bioc 3.24)cBioPortalData-2.24.0(bioc 3.23)

softwareinfrastructurethirdpartyclientbioconductor-packagenci-itcru24ca289073

10.26 score 34 stars 4 packages 308 scripts 810 downloads 1 mentions 29 exports 135 dependencies

Last updated from:e8ba4ab351 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE240
linux-devel-x86_64OK486
source / vignettesOK449
linux-release-x86_64OK555
macos-release-arm64OK333
macos-oldrel-arm64OK356
windows-develOK416
windows-releaseOK463
windows-oldrelOK375
wasm-releaseOK202

Exports:allSamplescBioCachecBioDataPackcBioPortalcBioPortalDataclinicalDatacopyNumberDatadownloadStudyfetchDatagenePanelMoleculargenePanelsgeneTablegetDataByGenesgetGenePanelgetGenePanelMoleculargetSampleInfogetStudiesloadStudymolecularDatamolecularProfilesmutationDataoperationsqueryGeneTableremovePackCachesampleListssamplesInSampleListssearchOpssetCacheuntarStudy

Dependencies:abindAnnotationDbiAnVILAnVILBaseaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbslibcachemcigarilloclicliprcodetoolscommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydigestdplyrDTevaluatefastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsGCPtoolsgenericsGenomeInfoDbGenomicAlignmentsGenomicDataCommonsGenomicFeaturesGenomicRangesgluehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2IRangesjquerylibjsonliteKEGGRESTkeyringknitrlambda.rlaterlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeminiUIMultiAssayExperimentopensslotelpillarpkgconfigpngprettyunitsprogresspromisespurrrR6RaggedExperimentrapiclientrappdirsRcppRCurlreadrrestfulrRhtslibrjsonRJSONIOrlangrmarkdownRsamtoolsRSQLiteRTCGAToolboxrtracklayerrvestS4ArraysS4VectorssassselectrSeqinfoshinysnowsourcetoolsSparseArraystringistringrSummarizedExperimentsysTCGAutilstibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsvroomwithrxfunXMLxml2xtableXVectoryaml

cBioPortalData: Data Build Errors

Marcel Ramos & Levi Waldron

Rendered fromcBioPortalDataErrors.Rmdusingknitr::rmarkdownon Jun 08 2026.

Last update: 2025-07-21
Started: 2021-06-07

cBioPortalData: API Reference Guide for Devs

Marcel Ramos & Levi Waldron

Rendered fromcBioPortalRClient.Rmdusingknitr::rmarkdownon Jun 08 2026.

Last update: 2025-07-21
Started: 2019-04-29

cBioPortalData: User Guide

Marcel Ramos & Levi Waldron

Rendered fromcBioPortalData.Rmdusingknitr::rmarkdownon Jun 08 2026.

Last update: 2025-07-21
Started: 2019-12-12

cgdsr to cBioPortalData: Migration Tutorial

Karim Mezhoud & Marcel Ramos

Rendered fromcgdsrMigration.Rmdusingknitr::rmarkdownon Jun 08 2026.

Last update: 2025-07-21
Started: 2022-04-21

Readme and manuals

Help Manual

Help pageTopics
Manage cache / download directories for study datacBioCache removePackCache setCache
Obtain pre-packaged data from cBioPortal and represent as a MultiAssayExperiment objectcBioDataPack
The R interface to the cBioPortal API Data ServiceallSamples cBioPortal clinicalData copyNumberData fetchData genePanelMolecular genePanels geneTable getDataByGenes getGenePanel getGenePanelMolecular getSampleInfo getStudies molecularData molecularProfiles mutationData queryGeneTable sampleLists samplesInSampleLists searchOps
A class for representing the cBioPortal API protocol.cBioPortal cBioPortal-class operations,cBioPortal-method
Download data from the cBioPortal APIcBioPortalData
Manually download, untar, and load study tarballsdownloadStudy loadStudy untarStudy