To install this package, start R and enter:

## try http:// if https:// URLs are not supported

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


DOI: 10.18129/B9.bioc.TCGAbiolinks    

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

Bioconductor version: Release (3.5)

The aim of TCGAbiolinks is : i) facilitate the GDC 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) 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>, Tiago Chedraoui Silva <tiagochst at>

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


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


HTML R Script 1. Introduction
HTML R Script 2. Searching GDC database
HTML R Script 3. Downloading and preparing files for analysis
HTML R Script 4. Clinical data
HTML R Script 5. Mutation data
HTML R Script Working with TCGAbiolinks package
PDF   Reference Manual
Text   NEWS


biocViews DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneRegulation, MethylationArray, Network, Pathways, Sequencing, Software, Survival
Version 2.5.9
In Bioconductor since BioC 3.2 (R-3.2) (2 years)
License GPL (>= 3)
Depends R (>= 3.2)
Imports downloader (>= 0.4), survminer, grDevices, gridExtra, graphics, tibble, grid, GenomicRanges, XML (>= 3.98.0), data.table, EDASeq(>= 2.0.0), edgeR(>= 3.0.0), jsonlite (>= 1.0.0), plyr, knitr, methods, biomaRt, ggplot2, ggthemes, survival, stringr (>= 1.0.0), IRanges, scales, rvest (>= 0.3.0), stats, utils, selectr, S4Vectors, ComplexHeatmap(>= 1.10.2), R.utils, SummarizedExperiment(>= 1.4.0), genefilter, ConsensusClusterPlus, readr, RColorBrewer, doParallel, dplyr, GenomeInfoDb, GenomicFeatures, parallel, tools, xml2, httr (>= 1.2.1), matlab, circlize, ggrepel (>= 0.6.3)
Suggests png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, dnet, Biobase, affy, testthat, limma, pathview, clusterProfiler, igraph, supraHex
Depends On Me
Imports Me MoonlightR, SpidermiR, TCGAbiolinksGUI
Suggests Me
Build Report  

Package Archives

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

Source Package TCGAbiolinks_2.5.9.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) TCGAbiolinks_2.5.9.tgz
Source Repository git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

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