mutedpy is a python library that implements tools and machine learning models able to analyze mutational datasets of protein sequences and/or structures. We implement numerous shallow models targeted for datasets of sizes
- Neural Networks (feed-forward, convolutional, graph)
- linear models
- Gaussian processes
- utilizing different similarirty metrics
- amino-acid embeddings
- esm embeddings, data-driven embeddings
- geometric features
A significant part of the package is devolted to:
- simulation of directed evolution campaigns
- manipulation of sequence datasets:
- conversion between different formats
- scanning, enumeration seach
- data splitting train/test
First clone the repository:
git clone https://github.com/Mojusko/mutedpy
Inside the project directory, run
pip install -e .
The -e option installs the package in "editable" mode, where pip links to your local copy of the repository, instead of copying the files to the your site-packages directory. That way, a simple git pull will update the package.
The project requires Python 3.6, and the dependencies should be installed with the package (let me know if it doesn't work for you).
- 21/05/2024 - initial commit
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Classical: pytorch, cvxpy, numpy, scipy, sklearn, pymanopt, mosek, pandas
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Special: 1. pytorch-minimize https://github.com/rfeinman/pytorch-minimize 2. stpy https://github.com/mojusko/pytorch-minimize
Mojmir Mutny