Package: cBioPortalData 2.25.1

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], NCI [fnd]

cBioPortalData_2.25.1.tar.gz
cBioPortalData_2.25.1.zip(r-4.7)cBioPortalData_2.25.1.zip(r-4.6)cBioPortalData_2.25.1.zip(r-4.5)
cBioPortalData_2.25.1.tgz(r-4.6-any)cBioPortalData_2.25.1.tgz(r-4.5-any)
cBioPortalData_2.25.1.tar.gz(r-4.7-any)cBioPortalData_2.25.1.tar.gz(r-4.6-any)
cBioPortalData_2.25.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cBioPortalData/json (API)

# Install 'cBioPortalData' in R:
install.packages('cBioPortalData', repos = c('https://bioc.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

10.32 score 35 stars 4 packages 308 scripts 1 mentions 29 exports 135 dependencies

Last updated from:a9714e8ab9. Checks:1 FAILURE, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksFAILURE289
linux-devel-x86_64NOTE442
source / vignettesOK418
linux-release-x86_64NOTE490
macos-release-arm64NOTE258
macos-oldrel-arm64NOTE244
windows-develNOTE335
windows-releaseNOTE350
windows-oldrelNOTE339
wasm-releaseOK173

Exports:allSamplescBioCachecBioDataPackcBioPortalcBioPortalDataclinicalDatacopyNumberDatadownloadStudyfetchDatagenePanelMoleculargenePanelsgeneTablegetDataByGenesgetGenePanelgetGenePanelMoleculargetSampleInfogetStudiesloadStudymolecularDatamolecularProfilesmutationDataoperationsqueryGeneTableremovePackCachesampleListssamplesInSampleListssearchOpssetCacheuntarStudy

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

cBioPortalData: Data Build Errors
Loading | Overview | Data from the cBioPortal API (cBioPortalData()) | Packaged data from cBioDataPack() | sessionInfo
Rendered fromcBioPortalDataErrors.Rmdusingknitr::rmarkdown

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

cBioPortalData: API Reference Guide for Devs
Installation | Introduction | Overview | API representation | Operations | Searching through the API | Studies | Clinical Data | Molecular Profiles | Molecular Profile Data | Genes | All available genes | Gene Panels | Molecular Gene Panels | genePanelMolecular | getGenePanelMolecular | getDataByGenes | Samples | Sample List Identifiers | Sample Identifiers | All samples within a study ID | Info on Samples | Advanced Usage | Clearing the cache | sessionInfo
Rendered fromcBioPortalRClient.Rmdusingknitr::rmarkdown

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

cBioPortalData: User Guide
Installation | Introduction | Citations | Overview | Data Structures | Identifying available studies | Choosing download method | Two main functions | cBioDataPack: Obtain Study Data as Zipped Tarballs | cBioPortalData: Obtain data from the cBioPortal API | Considerations | metadata | Build prompts | Manual downloads | Clearing the cache | cBioDataPack | cBioPortalData | Example Analysis: Kaplan-Meier Plot | Data update requests | sessionInfo | References
Rendered fromcBioPortalData.Rmdusingknitr::rmarkdown

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

cgdsr to cBioPortalData: Migration Tutorial
Introduction | Loading the package | Discovering studies | cBioPortalData setup | cgdsr setup | Obtaining Cases | cBioPortalData (Cases) | Notes | sampleLists | samples from sampleLists | getSampleInfo | cgdsr (Cases) | getCaseLists and getClinicalData | Obtaining Clinical Data | cBioPortalData (Clinical) | All clinical data | By sample data | cgdsr (Clinical) | getClinicalData | Clinical Data Summary | Molecular or Genetic Profiles | cBioPortalData (molecularProfiles) | cgdsr (getGeneticProfiles) | Genomic Profile Data for a set of genes | cBioPortalData (Indentify samples and genes) | Convert hugoGeneSymbol to entrezGeneId | Obtain all samples in study | cgdsr (Profile Data) | Molecular Data with cBioPortalData | molecularData | getDataByGenes | cBioPortalData: the main end-user function | Mutation Data | cBioPortalData (mutationData) | cgdsr (getMutationData) | Copy Number Alteration (CNA) | cBioPortalData (CNA) | cgdsr (CNA) | Methylation Data | cBioPortalData (Methylation) | cgdsr (Methylation) | sessionInfo
Rendered fromcgdsrMigration.Rmdusingknitr::rmarkdown

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