terraTCGAdata

This is the released version of terraTCGAdata; for the devel version, see terraTCGAdata.

OpenAccess TCGA Data on Terra as MultiAssayExperiment

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DOI: 10.18129/B9.bioc.terraTCGAdata

Bioconductor version: Release (3.22)

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.

Author: Marcel Ramos [aut, cre] ORCID iD ORCID: 0000-0002-3242-0582

Maintainer: Marcel Ramos <marcel.ramos at sph.cuny.edu>

Citation (from within R, enter citation("terraTCGAdata")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("terraTCGAdata")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("terraTCGAdata")

Obtain Terra TCGA data as MultiAssayExperiment HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, Infrastructure, Software

Version 1.14.0

In Bioconductor since BioC 3.15 (R-4.2) (3.5 years)

License Artistic-2.0

Depends AnVILGCP, MultiAssayExperiment

Imports AnVIL, BiocFileCache, dplyr, GenomicRanges, methods, RaggedExperiment, readr, S4Vectors, stats, tidyr, TCGAutils, utils

System Requirements

URL https://github.com/waldronlab/terraTCGAdata

Bug Reports https://github.com/waldronlab/terraTCGAdata/issues

Suggests AnVILBase, knitr, rmarkdown, BiocStyle, withr, testthat (>= 3.0.0)

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package terraTCGAdata_1.14.0.tar.gz

Windows Binary (x86_64) terraTCGAdata_1.13.0.zip

macOS Binary (x86_64) terraTCGAdata_1.14.0.tgz

macOS Binary (arm64) terraTCGAdata_1.14.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/terraTCGAdata

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/terraTCGAdata

Bioc Package Browser https://code.bioconductor.org/browse/terraTCGAdata/

Package Short Url https://bioconductor.org/packages/terraTCGAdata/

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