curatedTCGAData

This package is for version 3.6 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: 3.6

This package provides publicly available data from The Cancer Genome Atlas (TCGA) Bioconductor MultiAssayExperiment class objects. These objects integrate multiple assays (e.g. RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. The MultiAssayExperiment class links assay barcodes with patient IDs, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire experiment.

Author: Marcel Ramos <marcel.ramos at roswellpark.org>, Levi Waldron <lwaldron.research at gmail.com>, Lucas Schiffer <schiffer.lucas at gmail.com>, Valerie Obenchain <valerie.obenchain at roswellpark.org>, Morgan Martin <martin.morgan at roswellpark.org>

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

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

Installation

To install this package, start R (version "3.4") 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

Reference Manual PDF
NEWS Text

Details

biocViews CancerData, ExperimentData, Homo_sapiens_Data, ReproducibleResearch
Version 1.0.3
License Artistic-2.0
Depends R (>= 3.4.0), MultiAssayExperiment
Imports AnnotationHub, ExperimentHub, S4Vectors, utils
System Requirements
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Suggests BiocStyle, knitr, readr, rmarkdown, testthat
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Package Archives

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

Source Package curatedTCGAData_1.0.3.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/
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