This repository tools the CIBERSORTx docker container as needed to reproduce the results in HARP: Platform Independent Deconvolution Tool (Nozari et al.)
The script run_cibersort.sh provides deconvolution with the official CIBERSORTx/fractions
docker container, that can be requested via the original web page https://cibersortx.stanford.edu
The main intention of the script is to have a local docker container with CIBERSORT running and provide .txt files as input resulting from
prior preprocessing steps.
In order to apply our script in your environment, fill out the template.env with your credentials and env variables and rename the file .env