This repository contains R scripts, RMarkdown reports and small data dependencies associated with the manuscript Foroutan M et al, The ratio of exhausted to resident infiltrating lymphocytes is prognostic for colorectal cancer patient outcome. CIR, 2021.

Available folders contain the below files:

• data: small data dependencies for each of the single cell and bulk data sets
• output: small data files obtained using the analysis pipelines
• report: several Rmarkdown (.Rmd) reports, containing teh main analyses codes. There are separate reports for each of the CD8, CD4, and NK cell, for training and testing the signatures in single-cell data sets, and for each of the TCGA and Marisa data. There are a few additional reports for comparing the signatures as well as for the survival analyses from independent datasets.
• script: some custom and collected functions used in this study. These scripts are sourced in the RMarkdown reports.

Please email [email protected] if you have any questions.

Overview of the study along with my acrylic painting inspired by this work, now on the cover of Cancer Immunology Research journal (the October issue, 2021).