mhcflurry

MHC I ligand prediction package with competitive accuracy and a fast and documented implementation.

MHCflurry supports Class I peptide/MHC binding affinity prediction using ensembles of allele-specific models. It runs on Python 2.7 and 3.4+ using the keras neural network library. It exposes command-line and Python library interfaces.

If you find MHCflurry useful in your research please cite:

O'Donnell, T. et al., 2017. MHCflurry: open-source class I MHC binding affinity prediction. bioRxiv. Available at: http://www.biorxiv.org/content/early/2017/08/09/174243.

Installation (pip)

Install the package:

$ pip install mhcflurry

Then download our datasets and trained models:

$ mhcflurry-downloads fetch

You can now generate predictions:

$ mhcflurry-predict \
       --alleles HLA-A0201 HLA-A0301 \
       --peptides SIINFEKL SIINFEKD SIINFEKQ \
       --out /tmp/predictions.csv
       
Wrote: /tmp/predictions.csv

See the documentation for more details.