Introduction
10 September 2018
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:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("TCGAbiolinks")- 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 Patched
## major 3
## minor 5.1
## year 2018
## month 07
## day 12
## svn rev 74967
## language R
## version.string R version 3.5.1 Patched (2018-07-12 r74967)
## nickname Feather Spray## [1] '2.8.4'