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)

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          4                           
## minor          2.1                         
## year           2022                        
## month          06                          
## day            23                          
## svn rev        82513                       
## language       R                           
## version.string R version 4.2.1 (2022-06-23)
## nickname       Funny-Looking Kid
## [1] '2.25.3'