Package: cBioPortalData 2.19.0

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_2.19.0.tar.gz
cBioPortalData_2.19.0.zip(r-4.5)cBioPortalData_2.19.0.zip(r-4.4)cBioPortalData_2.19.0.zip(r-4.3)
cBioPortalData_2.19.0.tgz(r-4.4-any)cBioPortalData_2.17.1.tgz(r-4.3-any)
cBioPortalData_2.19.0.tar.gz(r-4.5-noble)cBioPortalData_2.19.0.tar.gz(r-4.4-noble)
cBioPortalData_2.19.0.tgz(r-4.4-emscripten)cBioPortalData_2.19.0.tgz(r-4.3-emscripten)
cBioPortalData.pdf |cBioPortalData.html
cBioPortalData/json (API)
NEWS

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

Peer review:

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

On BioConductor:cBioPortalData-2.17.1(bioc 3.20)cBioPortalData-2.16.0(bioc 3.19)

softwareinfrastructurethirdpartyclientbioconductor-package

9.74 score 30 stars 4 packages 136 scripts 29 exports 135 dependencies

Last updated 11 days agofrom:aa8539fb9c. Checks:OK: 3 NOTE: 4. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winOKOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winNOTEOct 31 2024
R-4.3-macNOTEOct 21 2024

Exports:allSamplescBioCachecBioDataPackcBioPortalcBioPortalDataclinicalDatadownloadStudyfetchDatagenePanelMoleculargenePanelsgeneTablegetDataByGenesgetGenePanelgetGenePanelMoleculargetSampleInfogetStudiesloadStudymolecularDatamolecularProfilesmutationDataoperationsqueryGeneTableremoveDataCacheremovePackCachesampleListssamplesInSampleListssearchOpssetCacheuntarStudy

Dependencies:abindAnnotationDbiAnVILAnVILBaseaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobbslibcachemclicliprcodetoolscommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydigestdplyrDTevaluatefansifastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicDataCommonsGenomicFeaturesGenomicRangesgluehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2IRangesjquerylibjsonliteKEGGRESTknitrlambda.rlaterlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeminiUIMultiAssayExperimentopensslpillarpkgconfigplogrpngprettyunitsprogresspromisespurrrR6RaggedExperimentrapiclientrappdirsRcppRCurlreadrrestfulrRhtslibrjsonRJSONIOrlangrmarkdownRsamtoolsRSQLiteRTCGAToolboxrtracklayerrvestS4ArraysS4VectorssassselectrshinysnowsourcetoolsSparseArraystringistringrSummarizedExperimentsysTCGAutilstibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsvroomwithrxfunXMLxml2xtableXVectoryamlzlibbioc

cBioPortalData: Data Build Errors

Rendered fromcBioPortalDataErrors.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2021-06-18
Started: 2021-06-07

cBioPortalData: API Reference Guide for Devs

Rendered fromcBioPortalRClient.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2023-10-16
Started: 2019-04-29

cBioPortalData: User Guide

Rendered fromcBioPortalData.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-02-02
Started: 2019-12-12

cgdsr to cBioPortalData: Migration Tutorial

Rendered fromcgdsrMigration.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-01-16
Started: 2022-04-21

Readme and manuals

Help Manual

Help pageTopics
Manage cache / download directories for study datacBioCache removeDataCache 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 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