https://github.com/const-ae/linear_perturbation_prediction-paper
https://github.com/const-ae/linear_perturbation_prediction-paper
Science Score: 39.0%
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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✓DOI references
Found 4 DOI reference(s) in README -
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○Scientific vocabulary similarity
Low similarity (7.0%) to scientific vocabulary
Last synced: 10 months ago
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JSON representation
Repository
Basic Info
- Host: GitHub
- Owner: const-ae
- License: mit
- Language: HTML
- Default Branch: main
- Size: 60.8 MB
Statistics
- Stars: 23
- Watchers: 3
- Forks: 4
- Open Issues: 2
- Releases: 3
Created almost 2 years ago
· Last pushed 12 months ago
Metadata Files
Readme
License
README.md
Code repository for Deep learning-based predictions of gene perturbation effects do not yet outperform simple linear baselines
This repository contains the code to reproduce our analysis from
Deep learning-based predictions of gene perturbation effects do not yet outperform simple linear baselines. Constantin Ahlmann-Eltze, Wolfgang Huber, Simon Anders. Nature Methods 2025; doi: https://doi.org/10.1038/s41592-025-02772-6
A copy of the code is permanently archived at https://doi.org/10.5281/zenodo.14832393.
- 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
Owner
- Name: Constantin
- Login: const-ae
- Kind: user
- Location: Heidelberg, Germany
- Company: EMBL
- Website: https://twitter.com/const_ae
- Repositories: 64
- Profile: https://github.com/const-ae
PhD Student, Biostats, R
GitHub Events
Total
- Create event: 4
- Release event: 2
- Issues event: 4
- Watch event: 34
- Issue comment event: 5
- Push event: 7
- Pull request event: 2
- Fork event: 7
Last Year
- Create event: 4
- Release event: 2
- Issues event: 4
- Watch event: 34
- Issue comment event: 5
- Push event: 7
- Pull request event: 2
- Fork event: 7
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 4
- Total pull requests: 2
- Average time to close issues: 2 months
- Average time to close pull requests: 2 days
- Total issue authors: 4
- Total pull request authors: 1
- Average comments per issue: 1.75
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 4
- Pull requests: 2
- Average time to close issues: 2 months
- Average time to close pull requests: 2 days
- Issue authors: 4
- Pull request authors: 1
- Average comments per issue: 1.75
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- MUCDK (1)
- HelloWorldLTY (1)
- vjcitn (1)
- ekernf01 (1)
Pull Request Authors
- ArianAmani (2)