Companion code repository for: "A quantitative analysis of the interplay of environment, neighborhood and cell state in 3D spheroids"

This contains the complete snakemake workflow used to derive the results from raw data stored on Zenodo for the publication:

"A quantitative analysis of the interplay of environment, neighborhood and cell state in 3D spheroids"

https://www.biorxiv.org/content/10.1101/2020.07.24.219659v1

Github Repository: https://github.com/BodenmillerGroup/SpheroidPublication

In addition to the Github repository, this archive also contains all the Singularity containers used for the analysis.