TCGAbiolinks_examples

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TCGAbiolinks_examples

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repository with the scripts to run examples of the publications with new functionalities of TCGAbiolinks

// repository documentation

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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, elenap@cancer.dk, Antonio Colaprico, , axc1833@med.miami.edu

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.

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