terraTCGAdata

DOI: 10.18129/B9.bioc.terraTCGAdata  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see terraTCGAdata.

OpenAccess TCGA Data on Terra as MultiAssayExperiment

Bioconductor version: 3.16

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.ramosperez at roswellpark.org>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Obtain Terra TCGA data as MultiAssayExperiment
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, Infrastructure, Software
Version	1.2.0
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
License	Artistic-2.0
Depends	R (>= 4.2.0), AnVIL, MultiAssayExperiment
Imports	BiocFileCache, dplyr, GenomicRanges, methods, RaggedExperiment, readr, S4Vectors, stats, tidyr, TCGAutils, utils
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, withr, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/waldronlab/terraTCGAdata
BugReports	https://github.com/waldronlab/terraTCGAdata/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	terraTCGAdata_1.2.0.tar.gz
Windows Binary	terraTCGAdata_1.2.0.zip (64-bit only)
macOS Binary (x86_64)	terraTCGAdata_1.2.0.tgz
macOS Binary (arm64)
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