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

This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see TCGAbiolinks.

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

Bioconductor version: 3.4

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 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

HTML R Script Introduction
HTML R Script TCGAbiolinks: Clinical data
HTML R Script TCGAbiolinks: Downloading and preparing files for analysis
HTML R Script TCGAbiolinks: Mutation data
HTML R Script TCGAbiolinks: Searching GDC database
HTML R Script Working with TCGAbiolinks package
PDF Reference Manual
Text NEWS

Details

biocViews DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneRegulation, MethylationArray, Network, Pathways, Sequencing, Software, Survival
Version 2.2.10
In Bioconductor since BioC 3.2 (R-3.2) (1.5 years)
License GPL (>= 3)
Depends R (>= 3.2)
Imports downloader (>= 0.4), survminer, grDevices, gridExtra, graphics, tibble, GenomicRanges, XML (>= 3.98.0), Biobase, affy, xtable, data.table, EDASeq(>= 2.0.0), edgeR(>= 3.0.0), jsonlite (>= 1.0.0), plyr, c3net, minet, knitr, methods, biomaRt, gplots, ggplot2, ggthemes, survival, stringr (>= 1.0.0), IRanges, scales, rvest (>= 0.3.0), stats, utils, dnet, igraph, selectr, supraHex, S4Vectors, ComplexHeatmap(>= 1.10.2), R.utils, SummarizedExperiment(>= 1.4.0), limma, genefilter, ConsensusClusterPlus, readr, RColorBrewer, doParallel, dplyr, clusterProfiler, pathview, parallel, xml2, httr (>= 1.2.1), parmigene, matlab, circlize, ggrepel (>= 0.6.3)
LinkingTo
Suggests testthat, png, BiocStyle, rmarkdown, devtools
SystemRequirements
Enhances
URL https://github.com/BioinformaticsFMRP/TCGAbiolinks
BugReports https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues
Depends On Me
Imports Me MoonlightR, SpidermiR
Suggests Me
Build Report

Package Archives

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

Package Source TCGAbiolinks_2.2.10.tar.gz
Windows Binary TCGAbiolinks_2.2.10.zip
Mac OS X 10.9 (Mavericks) TCGAbiolinks_2.2.10.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/TCGAbiolinks/tree/release-3.4
Package Short Url http://bioconductor.org/packages/TCGAbiolinks/
Package Downloads Report Download Stats

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