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.

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:
  • Development version:

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:

Session info

##                _                           
## platform       x86_64-pc-linux-gnu         
## arch           x86_64                      
## os             linux-gnu                   
## system         x86_64, linux-gnu           
## status                                     
## major          3                           
## minor          4.3                         
## year           2017                        
## month          11                          
## day            30                          
## svn rev        73796                       
## language       R                           
## version.string R version 3.4.3 (2017-11-30)
## nickname       Kite-Eating Tree
## [1] '2.6.12'