This repository contains code, conda environments, and step-by-instructions to reproduce the analysis published in Perino et al, 2018
Minor differences in the results and from the original 2018 code might be present as this repository has been created post-publication in 2022.
To reproduce the analysis install the conda environment envs/Perino_2018.yml and follow the instructions in the notebooks/html files in src/notebooks
All notebooks are meant to be run with with the environment envs/Perino_2018.yml installed and activated.
Environments with *snakemake* in the name are required for running the snakemake pipelines but do not need to be installed manually.
For enquiries/clarifications write to matteo dot perino at embl dot de