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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>, Tiago Chedraoui Silva <tiagochst at>

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


To install this package, start R and enter:

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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


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)
Suggests testthat, png, BiocStyle, rmarkdown, devtools
Depends On Me
Imports Me MoonlightR, SpidermiR
Suggests Me
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