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.

News


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)

Installation


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

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          4                           
## minor          3.1                         
## year           2023                        
## month          06                          
## day            16                          
## svn rev        84548                       
## language       R                           
## version.string R version 4.3.1 (2023-06-16)
## nickname       Beagle Scouts
packageVersion("TCGAbiolinks")
## [1] '2.28.4'