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.
You can install the stable version from Bioconductor, or the development version using:
source("https://bioconductor.org/biocLite.R")
biocLite("TCGAbiolinks")
devtools::install_github('BioinformaticsFMRP/TCGAbiolinks')
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/
Please use Github issues if you want to file bug reports or feature requests.
The examples in this tutorial use the following libraries:
library(TCGAbiolinks)
library(dplyr)
library(DT)
version
## _
## platform x86_64-pc-linux-gnu
## arch x86_64
## os linux-gnu
## system x86_64, linux-gnu
## status
## major 3
## minor 4.1
## year 2017
## month 06
## day 30
## svn rev 72865
## language R
## version.string R version 3.4.1 (2017-06-30)
## nickname Single Candle
packageVersion("TCGAbiolinks")
## [1] '2.5.9'