Package: terraTCGAdata 1.11.0
Marcel Ramos
terraTCGAdata: OpenAccess TCGA Data on Terra as MultiAssayExperiment
Leverage the existing open access TCGA data on Terra with well-established Bioconductor infrastructure. Make use of the Terra data model without learning its complexities. With a few functions, you can copy / download and generate a MultiAssayExperiment from the TCGA example workspaces provided by Terra.
Authors:
terraTCGAdata_1.11.0.tar.gz
terraTCGAdata_1.11.0.zip(r-4.5)terraTCGAdata_1.11.0.zip(r-4.4)terraTCGAdata_1.9.1.zip(r-4.3)
terraTCGAdata_1.11.0.tgz(r-4.4-any)terraTCGAdata_1.9.1.tgz(r-4.3-any)
terraTCGAdata_1.11.0.tar.gz(r-4.5-noble)terraTCGAdata_1.11.0.tar.gz(r-4.4-noble)
terraTCGAdata_1.11.0.tgz(r-4.4-emscripten)terraTCGAdata_1.9.1.tgz(r-4.3-emscripten)
terraTCGAdata.pdf |terraTCGAdata.html✨
terraTCGAdata/json (API)
NEWS
| # Install 'terraTCGAdata' in R: |
| install.packages('terraTCGAdata', repos = c('https://waldronlab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/waldronlab/terratcgadata/issues
On BioConductor:terraTCGAdata-1.9.2(bioc 3.20)terraTCGAdata-1.8.0(bioc 3.19)
softwareinfrastructuredataimportbioconductor-package
Last updated 23 days agofrom:3e2116729e. Checks:OK: 7. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | OK | Oct 31 2024 |
| R-4.5-linux | OK | Oct 30 2024 |
| R-4.4-win | OK | Oct 31 2024 |
| R-4.4-mac | OK | Oct 31 2024 |
| R-4.3-win | OK | Sep 21 2024 |
| R-4.3-mac | OK | Sep 21 2024 |
Exports:getAssayDatagetAssayTablegetClinicalgetClinicalTablegetTCGAdatalistsampleTypesTableselectTCGAworkspaceterraTCGAdataterraTCGAworkspace
Dependencies:abindAnnotationDbiAnVILAnVILBaseAnVILGCPaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobbslibcachemclicliprcodetoolscommonmarkcpp11crayoncrosstalkcurlDBIdbplyrDelayedArraydigestdplyrDTevaluatefansifastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicDataCommonsGenomicFeaturesGenomicRangesgluehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2IRangesjquerylibjsonliteKEGGRESTknitrlambda.rlaterlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeminiUIMultiAssayExperimentopensslpillarpkgconfigplogrpngprettyunitsprogresspromisespurrrR6RaggedExperimentrapiclientrappdirsRcppRCurlreadrrestfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorssassselectrshinysnowsourcetoolsSparseArraystringistringrSummarizedExperimentsysTCGAutilstibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsvroomwithrxfunXMLxml2xtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Obtain assay datasets from Terra | getAssayData |
| Obtain a reference table for assay data in the Terra data model | getAssayTable |
| Obtain clinical data | getClinical |
| Obtain the reference table for clinical data | getClinicalTable |
| Import Terra TCGA data as a list | getTCGAdatalist |
| Get an overview of the samples available in the workspace | sampleTypesTable |
| Obtain a MultiAssayExperiment from the Terra workspace | terraTCGAdata |
| Obtain or set the Terra Workspace Project Dataset | selectTCGAworkspace terraTCGAworkspace |
