Introduction

TCGAbiolinks is able to access The National Cancer Institute (NCI) Genomic Data Commons (GDC) thorough its
GDC Application Programming Interface (API) to search, download and prepare relevant data for analysis in R.

Citation

If you use TCGAbiolinks, please cite:

• Colaprico, Antonio, et al. “TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data.” Nucleic acids research 44.8 (2015): e71-e71.
• Silva, Tiago C., et al. “TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages.” F1000Research 5 (2016). (https://f1000research.com/articles/5-1542/v2)
• Mounir, Mohamed, et al. “New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx.” PLoS computational biology 15.3 (2019): e1006701. (https://doi.org/10.1371/journal.pcbi.1006701)

Other useful links

• Gao, Galen F., et al. “Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data.” Cell systems 9.1 (2019): 24-34. (https://doi.org/10.1016/j.cels.2019.06.006)

• TCGA Workflow Analyze cancer genomics and epigenomics data using Bioconductor packages: http://bioconductor.org/packages/TCGAWorkflow/

Installation

R

You can install the stable version from Bioconductor. If you are having issues with the stable version, try using the development version.

• Stable version:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("TCGAbiolinks")

• Development version:

devtools::install_github('BioinformaticsFMRP/TCGAbiolinks')

Docker image

If you prefer to use docker, TCGAbiolinks and TCGAbiolinksGUI are available as Docker image (self-contained environments that contain everything needed to run the software), which can be easily run on Mac OS, Windows and Linux systems.

This PDF show how to install and execute the image.

The image can be obtained from Docker Hub: https://hub.docker.com/r/tiagochst/tcgabiolinksgui/

For more information please check: https://docs.docker.com/ and https://www.bioconductor.org/help/docker/

Question and issues

Please use Github issues if you want to file bug reports or feature requests.

Required libraries

The examples in this tutorial use the following libraries:

library(TCGAbiolinks)
library(dplyr)
library(DT)

Session info

version

##                _                           
## platform       x86_64-pc-linux-gnu         
## arch           x86_64                      
## os             linux-gnu                   
## system         x86_64, linux-gnu           
## status                                     
## major          3                           
## minor          6.1                         
## year           2019                        
## month          07                          
## day            05                          
## svn rev        76782                       
## language       R                           
## version.string R version 3.6.1 (2019-07-05)
## nickname       Action of the Toes

packageVersion("TCGAbiolinks")

## [1] '2.12.6'