curatedTCGAData
Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
Bioconductor version: 3.23 · Package version: 1.34.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("curatedTCGAData")Details
| Maintainer | Marcel Ramos <marcel.ramos@sph.cuny.edu> |
| Author | Marcel Ramos [aut, cre] (ORCID: <https://orcid.org/0000-0002-3242-0582>), Levi Waldron [ctb], Lucas Schiffer [ctb], Ludwig Geistlinger [ctb], Valerie Obenchain [ctb], Martin Morgan [ctb], NCI [fnd] (GrantNo.: U24CA289073) |
| License | Artistic-2.0 |
| Bug Reports | https://github.com/waldronlab/curatedTCGAData/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | CancerData, ExperimentData, ExperimentHub, Homo_sapiens_Data, ReproducibleResearch |
| Package Short Url | https://bioconductor.org/packages/curatedTCGAData/ |
Citation
From within R, enter citation("curatedTCGAData"):
Marcel Ramos. curatedTCGAData: Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects. doi:10.18129/B9.bioc.curatedTCGAData, R package version 1.34.0, https://bioconductor.org/packages/curatedTCGAData.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | curatedTCGAData_1.34.0.tar.gz |
Dependencies
Depends: R (>= 4.5.0), MultiAssayExperiment
Imports: AnnotationHub, ExperimentHub, HDF5Array, methods, S4Vectors, stats, SummarizedExperiment, utils
Suggests: BiocStyle, knitr, RaggedExperiment, readr, rmarkdown, TCGAutils, testthat
Reverse dependencies
Imports Me (1): AMARETTO
Suggests Me (4): CNVRanger, glmSparseNet, imageFeatureTCGA, TCGAutils