https://github.com/const-ae/linear_perturbation_prediction-paper

https://github.com/const-ae/linear_perturbation_prediction-paper

Last synced: 9 days ago
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• Host: GitHub
• URL: https://github.com/const-ae/linear_perturbation_prediction-paper
• Owner: const-ae
• License: mit
• Created: 2024-08-28T10:05:11.000Z (4 months ago)
• Default Branch: main
• Last Pushed: 2024-09-30T14:52:22.000Z (3 months ago)
• Last Synced: 2024-11-06T14:00:50.369Z (about 2 months ago)
• Language: HTML
• Size: 20.8 MB
• Stars: 15
• Watchers: 2
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

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README

        
# 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

  - [Double Perturbation Analysis](https://htmlpreview.github.io/?https://github.com/const-ae/linear_perturbation_prediction-Paper/blob/main/notebooks/double_perturbation_analysis.html)

  - [Single Perturbation Analysis](https://htmlpreview.github.io/?https://github.com/const-ae/linear_perturbation_prediction-Paper/blob/main/notebooks/single_perturbation_analysis.html)

- 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](https://github.com/const-ae/MyWorkflowManager) workflow manager