GEMDeCan: Gene Expression and Methylation based Deconvolution for Cancer
You will find here two snakemake pipelines to process and perform deconvolution on gene expression and methylation data, in the respectively named folders.
Each pipeline comes with a readme detailing its installation and usage.
The code to reproduce all figures is available in this repository under Paper_Figure_code.Rmd.
All data to reproduce those figures are freely available on Figshare :
https://figshare.com/account/home#/projects/134069
To cite the pipeline, refer to our paper on BiorXiv :
GEM-DeCan: Improved tumor immune microenvironment profiling through novel gene expression and DNA methylation signatures predicts immunotherapy response
Ting Xie, Jacobo Solorzano, Miguel Madrid-Mencía, Abdelmounim Essabbar, Julien Pernet, Mei-Shiue Kuo, Alexis Hucteau, Alexis Coullomb, Nina Verstraete, Olivier Delfour, Francisco Cruzalegui, Vera Pancaldi
bioRxiv 2021.04.09.439207; doi: https://doi.org/10.1101/2021.04.09.439207