This is the release of the full scripts used for the paper:
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
Please cite this article if you re-use any of the data or code.
Changelog:
Tested the workflow with the latest snakemake and added an extra rule to export the processed data as a zip.