mhcflurry
Peptide-MHC binding affinity prediction
Quickstart
Set up the Python environment:
# (set up environment)
pip install scipy Cython
pip install h5py
python setup.py developDownload, Normalize, and Combine Training Data:
(make sure you have wget available, e.g. brew install wget on Mac OS X)
script/download-iedb.sh
script/download-peters-2013-dataset.sh
script/create-iedb-class1-dataset.py
script/create-combined-class1-dataset.pyTrain Neural Network Models
mhcflurry-train-class1-allele-specific-models.pyThis will train separate models for each HLA type.
Making predictions
from mhcflurry import predict
predict(alleles=['A0201'], peptides=['SIINFEKL']) Allele Peptide Prediction
0 A0201 SIINFEKL 586.730529