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terraTCGAdata

OpenAccess TCGA Data on Terra as MultiAssayExperiment


Bioconductor version: Release (3.18)

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]

Maintainer: Marcel Ramos <marcel.ramos at roswellpark.org>

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

Installation

To install this package, start R (version "4.3") 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

Details

biocViews DataImport, Infrastructure, Software
Version 1.6.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License Artistic-2.0
Depends R (>= 4.2.0), AnVIL, MultiAssayExperiment
Imports 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
See More
Suggests knitr, rmarkdown, BiocStyle, withr, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package terraTCGAdata_1.6.0.tar.gz
Windows Binary terraTCGAdata_1.6.0.zip
macOS Binary (x86_64) terraTCGAdata_1.6.0.tgz
macOS Binary (arm64) terraTCGAdata_1.6.0.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/
Package Downloads Report Download Stats