Installation | Citing curatedTCGAData | Data versions | Version 2.0.1 | Data source | Downloading datasets | Caveats for working with TCGA data | ACC dataset example | Subtype information | Typical clinical variables | Identifying samples in Assays | Separating samples | TCGAprimaryTumors convenience | Keeping colData in an extracted Assay | Example use of RaggedExperiment | Exporting Data | Session Information | References
Package: curatedTCGAData 1.35.1
Marcel Ramos
curatedTCGAData: Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
This package provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. MultiAssayExperiment integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-'omics experiment.
Authors:
curatedTCGAData_1.35.1.tar.gz
curatedTCGAData_1.35.1.tar.gz(r-4.7-any)curatedTCGAData_1.35.1.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
curatedTCGAData/json (API)
| # Install 'curatedTCGAData' in R: |
| install.packages('curatedTCGAData', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/waldronlab/curatedtcgadata/issues
On BioConductor:curatedTCGAData-1.35.0(data/experiment 3.24)curatedTCGAData-1.34.0(data/experiment 3.23)
homo_sapiens_datareproducibleresearchcancerdataexperimenthubbioconductor-packageu24ca289073datapkg
Last updated from:dab8efa4f6. Checks:1 WARNING, 2 NOTE, 1 OK. Indexed: yes.
This is a data package. Data packages may be large and do not get checked across all platforms.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 245 | ||
| linux-devel | NOTE | 434 | ||
| source / vignettes | OK | 483 | ||
| linux-release | NOTE | 425 |
Exports:curatedTCGAData
Dependencies:abindAnnotationDbiAnnotationHubaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsbiocmakeBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrDelayedArraydir.expirydplyrExperimentHubfastmapfilelockgenericsGenomicRangesglueh5mreadHDF5Arrayhttrhttr2IRangesjsonliteKEGGRESTlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeMultiAssayExperimentopensslpillarpkgconfigpngpurrrR6rappdirsrhdf5rhdf5filtersRhdf5librlangRSQLiteS4ArraysS4VectorsSeqinfoSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXVectoryaml
