To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TCGAbiolinks")

In most cases, you don't need to download the package archive at all.

TCGAbiolinks

   

TCGAbiolinks: An R/Bioconductor package for integrative analysis with TCGA data

Bioconductor version: 3.2

The aim of TCGAbiolinks is : i) facilitate the TCGA open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) allow the user to download a specific version of the data and thus to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.

Author: Antonio Colaprico, Tiago Chedraoui Silva, Catharina Olsen, Luciano Garofano, Davide Garolini, Claudia Cava, Thais Sabedot, Tathiane M. Malta, Stefano M. Pagnotta, Isabella Castiglioni, Michele Ceccarelli, Gianluca Bontempi, Houtan Noushmehr

Maintainer: Antonio Colaprico <antonio.colaprico at ulb.ac.be>, Tiago Chedraoui Silva <tiagochst at usp.br>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TCGAbiolinks")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("TCGAbiolinks")

 

HTML Working with TCGAbiolinks package
PDF   Reference Manual
Text   NEWS

Details

biocViews DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneRegulation, MethylationArray, Network, Pathways, Software, Survival
Version 1.0.10
In Bioconductor since BioC 3.2 (R-3.2) (0.5 years)
License GPL (>= 3)
Depends R (>= 3.2)
Imports downloader (>= 0.4), GGally, grDevices, graphics, GenomicRanges, XML, Biobase, affy, heatmap.plus, xtable, data.table, EDASeq(>= 2.0.0), RCurl, edgeR(>= 3.0.0), rjson, plyr, CNTools, cghMCR, biomaRt, coin, gplots, ggplot2, survival, stringr (>= 1.0.0), IRanges, scales, rvest, stats, utils, dnet, igraph, supraHex, S4Vectors, SummarizedExperiment, BiocGenerics, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, limma, knitr, devtools, genefilter, ConsensusClusterPlus, RColorBrewer, doParallel, dplyr, parallel, xml2
LinkingTo
Suggests testthat, png, BiocStyle, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source TCGAbiolinks_1.0.10.tar.gz
Windows Binary TCGAbiolinks_1.0.10.zip
Mac OS X 10.6 (Snow Leopard) TCGAbiolinks_1.0.1.tgz
Mac OS X 10.9 (Mavericks) TCGAbiolinks_1.0.10.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/TCGAbiolinks/tree/release-3.2
Package Short Url http://bioconductor.org/packages/TCGAbiolinks/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center