This repository contains all scripts to reproduce the associated publication.
normancontains all analyses related to "Learning and exploring perturbation representations with pertpy".mcfarlandcontains all analyses related to "Pertpy streamlines discovery for complex perturbation experiments"zhangcontains all analyses related to "Pertpy enables deciphering effects of perturbations on cellular systems".
The benchmark folder has individual tool specific subfolders that each contain a Conda *_environment.yml file together with a *_comparison notebook where the original implementation is compared against the implementation in pertpy with a suitable metric.
The benchmark folder further contains all scripts that were run using a Snakemake pipeline to evaluate the runtime requirements of the tools.
In particular, the visualize_benchmark_results.ipynb notebook aggregates all results from the benchmarking_table.csv which is stored in the tables folder to create the figure.