Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark

Repository associated to the publication:

New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx Mohamed Mounir, Marta Lucchetta, Tiago C Silva, Catharina Olsen, Gianluca Bontempi, Xi Chen, Houtan Noushmehr, Antonio Colaprico, Elena Papaleo* PLoS Comput Biol. 2019 Mar 5;15(3):e1006701. doi: 10.1371/journal.pcbi.1006701

corresponding author: Elena Papaleo, [email protected], Antonio Colaprico, , [email protected]

This repository contains the scripts to run the three cases study presented in the manuscript, which have the purposes to serve as examples for the new functionalities implemented in TCGAbiolinks

Requirements:

R version 3.5 or higher Rstudio version 1.1.383 or higher
Bioconductor version 3.7 or higher

Other packages required:

BIOCONDUCTOR:

TCGAbiolinks SummarizedExperiment limma biomaRt recount TCGAutils

CRAN plyr UpSetR ggplot2 NOTES:

We suggest to use Rstudio to run the scripts of interest so that you can follow the analyses one line at the time and digest the results.