curatedTCGAData

DOI: 10.18129/B9.bioc.curatedTCGAData    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see curatedTCGAData.

Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects

Bioconductor version: 3.10

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.

Author: Marcel Ramos [aut, cre], Levi Waldron [ctb], Lucas Schiffer [ctb], Ludwig Geistlinger [ctb], Valerie Obenchain [ctb], Martin Morgan [ctb]

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("curatedTCGAData")

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("curatedTCGAData")

 

HTML	R Script	curatedTCGAData
PDF		Reference Manual
Text		NEWS

Details

biocViews	CancerData, ExperimentData, ExperimentHub, Homo_sapiens_Data, ReproducibleResearch
Version	1.8.1
License	Artistic-2.0
Depends	R (>= 3.5.0), MultiAssayExperiment
Imports	AnnotationHub, ExperimentHub, HDF5Array, S4Vectors, stats, SummarizedExperiment, utils
LinkingTo
Suggests	BiocStyle, knitr, readr, rmarkdown, TCGAutils, testthat
SystemRequirements
Enhances
URL
BugReports	https://github.com/waldronlab/curatedTCGAData/issues
Depends On Me
Imports Me	AMARETTO, BiocOncoTK
Suggests Me	CNVRanger, deco, glmSparseNet, TCGAutils
Links To Me
Build Report

Package Archives

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

Source Package	curatedTCGAData_1.8.1.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository	git clone https://git.bioconductor.org/packages/curatedTCGAData
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/curatedTCGAData
Package Short Url	https://bioconductor.org/packages/curatedTCGAData/
Package Downloads Report	Download Stats