MHCnuggets: Neoantigen peptide MHC binding prediction for class I and II
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:
- [MHCnuggets with command line interface](https://github.com/KarchinLab/mhcnuggets/wiki/Creating-a-mhcnuggets-docker-container-with-command-line-interface)
- [MHCnuggets with Jupyter Notebook interface](https://github.com/KarchinLab/mhcnuggets/wiki/Creating-a-mhcnuggets-docker-container-with-Jupyter-Notebook-interface)
- [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 `
You might want to check if the Keras backend is configured to use the Tensforflow backend.
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