Code repository for Deep learning-based predictions of gene perturbation effects do not yet outperform simple linear methods
This repository contains the code to reproduce our analysis.
- The notebooks folder contains the R scripts used for the analysis and to make the figures
- The benchmark folder contains the scripts to reproduce the benchmark results
- The benchmark/src contains individual scripts to run each method
- The benchmark/conda_environments and benchmark/renv contain the details about the software versions
- The benchmark/submission contains the script to launch the scripts using my custom workflow manager