This repository contains all scripts available to reproduce results from Carraro et al, eLife 2022, DOI: XXX. Related R environments with associated Session Info are freely accessible on Zenodo (DOI: 10.5281/zenodo.6984701). Separate annotated scripts and environments are available for the analysis of 3-chloropiperidines (3-CePs, M and B) versus cisplatin. For both, markdown files are provided to process the RNA-seq and ATAC-seq datasets, to execute the horizontal integration (RNA-seq and ATAC-seq, based on hCoCena), the vertical integration (based on vCoCena) and the sensitivity prediction.

To ensure the reproducibility of the manuscript results, all the analyses were conducted within a containerized environment (Docker). RNA-seq and ATAC-seq analyses were performed with the docker image jsschrepping/r_docker:jss_R362 (https://hub.docker.com/r/jsschrepping/r_docker). The rest of the analysis was conducted with the image lorenzobonaguro/cocena:v3 (https://hub.docker.com/r/lorenzobonaguro/cocena) for compatibility with the CoCena pipeline.