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

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 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	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

Details

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)
LinkingTo
Suggests	png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, dnet, Biobase, affy, testthat, limma, pathview, clusterProfiler, igraph, supraHex
SystemRequirements
Enhances
URL	https://github.com/BioinformaticsFMRP/TCGAbiolinks
BugReports	https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues
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	TCGAbiolinks_2.5.9.zip
Mac OS X 10.11 (El Capitan)	TCGAbiolinks_2.5.9.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TCGAbiolinks
Package Short Url	http://bioconductor.org/packages/TCGAbiolinks/
Package Downloads Report	Download Stats

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