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MHCnuggets: Neoantigen peptide MHC binding prediction for class I and II

Project description

# MHCnuggets

Welcome to MHCnuggets! Presumably you’re here to do some peptide-MHC prediction and not because you were [hungry](https://www.mcdonalds.com/us/en-us/product/chicken-mcnuggets-4-piece.html).

### Usage ### For an overview of how to use MHCnuggets please refer to the Jupyter notebook called user_guide.ipynb in the repository

If you would like to use MHCnuggets as a docker container, there are several options:

  1. [MHCnuggets with command line interface](https://github.com/KarchinLab/mhcnuggets/wiki/Creating-a-mhcnuggets-docker-container-with-command-line-interface)
  2. [MHCnuggets with Jupyter Notebook interface](https://github.com/KarchinLab/mhcnuggets/wiki/Creating-a-mhcnuggets-docker-container-with-Jupyter-Notebook-interface)
  3. [MHCnuggets container for batch operations](https://github.com/KarchinLab/mhcnuggets/wiki/Creating-and-running-the-MHCnuggets-batch-container)

### Installation ###

MHCnuggets is pip installable as: `bash pip install mhcnuggets `

Required pacakges:

  • numpy
  • scipy
  • scikit-learn
  • pandas
  • tensorflow
  • keras

You might want to check if the Keras backend is configured to use the Tensforflow backend.

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