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

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Welcome to MHCnuggets! Presumably you're here to do some peptide-MHC prediction and not because you were hungry.


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

  2. MHCnuggets with Jupyter Notebook interface

  3. MHCnuggets container for batch operations


MHCnuggets is pip installable as:

pip install mhcnuggets

Required pacakges:

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

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

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