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"

Vito RT Zanotelli
Matthias Leutenegger
Xiao‐Kang Lun
Fanny Georgi
Natalie de Souza
Bernd Bodenmiller

Mol Syst Biol. (2020) 16: e9798
https://doi.org/10.15252/msb.20209798

Github Repository: https://github.com/BodenmillerGroup/SpheroidPublication/releases/tag/v1.1

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