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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 (3.18)

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 "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
curatedTCGAData HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CancerData, ExperimentData, ExperimentHub, Homo_sapiens_Data, ReproducibleResearch
Version 1.23.6
License Artistic-2.0
Depends R (>= 4.2.0), MultiAssayExperiment
Imports AnnotationHub, ExperimentHub, HDF5Array, methods, S4Vectors, stats, SummarizedExperiment, utils
Linking To
Suggests BiocStyle, knitr, RaggedExperiment, readr, rmarkdown, TCGAutils, testthat
System Requirements
Enhances
URL
Bug Reports https://github.com/waldronlab/curatedTCGAData/issues
See More
Depends On Me
Imports Me AMARETTO, BiocOncoTK
Suggests Me CNVRanger, dce, deco, glmSparseNet, IntOMICS, netDx, TCGAutils
Links To Me
Build Report  

Package Archives

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

Source Package curatedTCGAData_1.23.6.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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