News

• April 2022:
  • Started to add support for GENCODE v36 pipelines
  • Add stemness score functions
• December 2019:
  • Added support to non TCGA/TARGET projects - https://rpubs.com/tiagochst/TCGAbiolinks_RNA-seq_new_projects
  • Added support to linked Omics data retrieval - https://rpubs.com/tiagochst/linkedOmics
  • Included Glioma classifier from GUI to the main package - https://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/classifiers.html
• Added support to BCR Biotab clinical files
  
• Workshop materials (ATAC-seq, ELMER and TCGAbiolinks) were added to vignette (https://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html)

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)

Other useful links

• Gao, Galen F., et al. “Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data.” Cell systems 9.1 (2019): 24-34. (https://doi.org/10.1016/j.cels.2019.06.006)

• TCGA Workflow Analyze cancer genomics and epigenomics data using Bioconductor packages: http://bioconductor.org/packages/TCGAWorkflow/

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          4.2                         
## year           2024                        
## month          10                          
## day            31                          
## svn rev        87279                       
## language       R                           
## version.string R version 4.4.2 (2024-10-31)
## nickname       Pile of Leaves

packageVersion("TCGAbiolinks")

## [1] '2.35.0'