Package: cBioPortalData 2.17.1
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:
cBioPortalData_2.17.1.tar.gz
cBioPortalData_2.17.1.zip(r-4.5)cBioPortalData_2.17.1.zip(r-4.4)cBioPortalData_2.17.0.zip(r-4.3)
cBioPortalData_2.17.1.tgz(r-4.4-any)cBioPortalData_2.17.0.tgz(r-4.3-any)
cBioPortalData_2.17.1.tar.gz(r-4.5-noble)cBioPortalData_2.17.1.tar.gz(r-4.4-noble)
cBioPortalData_2.17.1.tgz(r-4.4-emscripten)cBioPortalData_2.17.0.tgz(r-4.3-emscripten)
cBioPortalData.pdf |cBioPortalData.html✨
cBioPortalData/json (API)
NEWS
| # 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-2.17.0(bioc 3.20)cBioPortalData-2.16.0(bioc 3.19)
Last updated 25 days agofrom:f431e08468. Checks:OK: 3 NOTE: 4. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 22 2024 |
| R-4.5-win | NOTE | Aug 22 2024 |
| R-4.5-linux | NOTE | Aug 22 2024 |
| R-4.4-win | NOTE | Aug 22 2024 |
| R-4.4-mac | NOTE | Aug 22 2024 |
| R-4.3-win | OK | Jul 22 2024 |
| R-4.3-mac | OK | Jul 22 2024 |
Exports:allSamplescBioCachecBioDataPackcBioPortalcBioPortalDataclinicalDatadownloadStudyfetchDatagenePanelMoleculargenePanelsgeneTablegetDataByGenesgetGenePanelgetGenePanelMoleculargetSampleInfogetStudiesloadStudymolecularDatamolecularProfilesmutationDataoperationsqueryGeneTableremoveDataCacheremovePackCachesampleListssamplesInSampleListssearchOpssetCacheuntarStudy
Dependencies:abindAnnotationDbiAnVILAnVILBaseaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobbslibcachemclicliprcodetoolscommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydigestdplyrDTevaluatefansifastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicDataCommonsGenomicFeaturesGenomicRangesgluehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2IRangesjquerylibjsonliteKEGGRESTknitrlambda.rlaterlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeminiUIMultiAssayExperimentopensslpillarpkgconfigplogrpngprettyunitsprogresspromisespurrrR6RaggedExperimentrapiclientrappdirsRcppRCurlreadrrestfulrRhtslibrjsonRJSONIOrlangrmarkdownRsamtoolsRSQLiteRTCGAToolboxrtracklayerrvestS4ArraysS4VectorssassselectrshinysnowsourcetoolsSparseArraystringistringrSummarizedExperimentsysTCGAutilstibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsvroomwithrxfunXMLxml2xtableXVectoryamlzlibbioc
cBioPortalData: Data Build Errors
Rendered fromcBioPortalDataErrors.Rmdusingknitr::rmarkdownon Aug 22 2024.Last update: 2021-06-18
Started: 2021-06-07
cBioPortalData: API Reference Guide for Devs
Rendered fromcBioPortalRClient.Rmdusingknitr::rmarkdownon Aug 22 2024.Last update: 2023-10-16
Started: 2019-04-29
cBioPortalData: User Guide
Rendered fromcBioPortalData.Rmdusingknitr::rmarkdownon Aug 22 2024.Last update: 2024-02-02
Started: 2019-12-12
cgdsr to cBioPortalData: Migration Tutorial
Rendered fromcgdsrMigration.Rmdusingknitr::rmarkdownon Aug 22 2024.Last update: 2024-01-16
Started: 2022-04-21
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Manage cache / download directories for study data | cBioCache removeDataCache removePackCache setCache |
| Obtain pre-packaged data from cBioPortal and represent as a MultiAssayExperiment object | cBioDataPack |
| The R interface to the cBioPortal API Data Service | allSamples 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 API | cBioPortalData |
| Manually download, untar, and load study tarballs | downloadStudy loadStudy untarStudy |
