curatedTCGAData

DOI: 10.18129/B9.bioc.curatedTCGAData    

This is the development version of curatedTCGAData; for the stable release version, see curatedTCGAData.

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

Bioconductor version: Development (3.9)

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>

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

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("curatedTCGAData", version = "3.9")

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 1.5.10
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
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_1.5.10.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 http://bioconductor.org/packages/curatedTCGAData/
Package Downloads Report Download Stats

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