Dynamic interferon beta signalling underlies treatment response to immune checkpoint therapy in cancer

Introduction

This repository contains the snakemake workflows for the RNAseq analysis for the manuscript. Each folder contains a snakemake workflow for the three major parts of the analysis, namely bulk RNAseq data, single RNAseq data and analysis of the human dataset from Bassez et al. (2021).

Attributions

This workflow uses custom code from Vesna Memisevic for constructing the HiveR object used for hiveplot visualisations.

References

1. Bassez, A., Vos, H., Van Dyck, L., Floris, G., Arijs, I., Desmedt, C., Boeckx, B., Vanden Bempt, M., Nevelsteen, I., Lambein, K., Punie, K., Neven, P., Garg, A. D., Wildiers, H., Qian, J., Smeets, A., & Lambrechts, D. (2021). A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer. Nature medicine, 27(5), 820–832. https://doi.org/10.1038/s41591-021-01323-8