Package: cBioPortalData 2.25.1

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://link-ny.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

8.67 score 35 stars 4 packages 308 scripts 29 exports 135 dependencies

Last updated from:a9714e8ab9. Checks:8 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR513
source / vignettesERROR340
linux-release-x86_64ERROR491
macos-release-arm64ERROR293
macos-oldrel-arm64ERROR266
windows-develERROR319
windows-releaseERROR346
windows-oldrelERROR347
wasm-releaseOK243

Exports:allSamplescBioCachecBioDataPackcBioPortalcBioPortalDataclinicalDatacopyNumberDatadownloadStudyfetchDatagenePanelMoleculargenePanelsgeneTablegetDataByGenesgetGenePanelgetGenePanelMoleculargetSampleInfogetStudiesloadStudymolecularDatamolecularProfilesmutationDataoperationsqueryGeneTableremovePackCachesampleListssamplesInSampleListssearchOpssetCacheuntarStudy

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

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