curatedTCGAData

DOI: 10.18129/B9.bioc.curatedTCGAData    

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

Bioconductor version: Release (3.14)

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 "4.1") and enter:

if (!require("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	1.16.0
License	Artistic-2.0
Depends	R (>= 3.5.0), MultiAssayExperiment
Imports	AnnotationHub, ExperimentHub, HDF5Array, methods, S4Vectors, stats, SummarizedExperiment, utils
LinkingTo
Suggests	BiocStyle, knitr, RaggedExperiment, readr, rmarkdown, TCGAutils, testthat
SystemRequirements
Enhances
URL
BugReports	https://github.com/waldronlab/curatedTCGAData/issues
Depends On Me
Imports Me	AMARETTO, BiocOncoTK
Suggests Me	CNVRanger, dce, deco, glmSparseNet, netDx, TCGAutils
Links To Me
Build Report

Package Archives

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

Source Package	curatedTCGAData_1.16.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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