DOI: 10.18129/B9.bioc.TCGAbiolinks    

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

Bioconductor version: Release (3.6)

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 10. TCGAbiolinks_Extension
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 6. Compilation of TCGA molecular subtypes
HTML R Script 7. Analyzing and visualizing TCGA data
HTML R Script 8. Case Studies
HTML R Script 9. Graphical User Interface (GUI)
PDF   Reference Manual
Text   NEWS


biocViews DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneRegulation, MethylationArray, Network, Pathways, Sequencing, Software, Survival
Version 2.6.12
In Bioconductor since BioC 3.2 (R-3.2) (2.5 years)
License GPL (>= 3)
Depends R (>= 3.2)
Imports downloader (>= 0.4), survminer, grDevices, dplyr, 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, GenomeInfoDb, GenomicFeatures, parallel, tools, sva, limma, xml2, httr (>= 1.2.1), matlab, circlize, ggrepel (>= 0.6.3)
Suggests png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, dnet, Biobase, affy, testthat, pathview, clusterProfiler, igraph, supraHex
Depends On Me
Imports Me ELMER, MoonlightR, SpidermiR, TCGAbiolinksGUI
Suggests Me
Build Report  

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Source Package TCGAbiolinks_2.6.12.tar.gz
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Mac OS X 10.11 (El Capitan) TCGAbiolinks_2.6.12.tgz
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