The pharmacogenomic assessment of molecular epithelial-mesenchymal transition signatures reveals drug susceptibilities in cancer cell lines

This repository contains the analysis steps for assessing epithelial-mesenchymal transition scores as predictive biomarkers (emtpb) for drug response in cancer cell lines.

Table of Contents

• Prerequisites
• Code
• Environment
• Usage
• Citation

Prerequisites

Most of the required software is available in a docker container. Furthermore, nextflow and charliecloud need to be installed for running the benchmarks.

Code

Pull the repository with

# Clone the repository
git clone https://github.com/mendenlab/emtpb.git

Environment

The required software for running the analysis is available on a docker container. It can be either pulled from dockerhub by typing docker pull aljoshoh/emtpb (recommended), or it can be rebuilt from scratch:

# Build and export container
cd emtpb/environment
docker build --no-cache -f Dockerfile -t "aljoshoh/emtpb" .
docker export $(docker create aljoshoh/emtpb) | gzip -c > metadata/emtpb.tar.gz

After having the container available, you can run the image by

docker run --rm -it -p 3838:3838 aljoshoh/emtpb /bin/bash

Within the image can run the analysis steps in scripts/. You can also run them within rstudio, which you can access by typing

/bin/start_rstudio 3838

while accessing the session in http://localhost:3838 with rstudio as username and the generated password.

Usage

The ordered analysis pipeline in scripts/ can be run within the created environment. Make sure to adjust your system paths in scripts/config.yaml. While each of the R scripts only needs to be run once, the benchmarks in scripts/02_benchmark_* will need to be run in batch mode using nextflow (with adjusted paths). Then, un each of the two benchmarks by:

# Run 1
cd nf
nextflow run train_chc.nf --file=scripts/02_benchmark_PANCAN.ipynb --amount=313600 --desc=exp3 -profile slurm -bg -with-trace -ansi-log false --Xms500M --Xmx2G > nf.log

# Run 2
cd nf_2
nextflow run train_chc.nf --file=scripts/02_benchmark_CI.ipynb --amount=156800 --desc=exp6 -profile slurm -bg -with-trace -ansi-log false --Xms500M --Xmx2G > nf.log

The figures for the manuscript can be reproduced by running paper/figures_02.Rmd.

Citation

This repository refers to our latest manuscript (citation pending).