EPIP

EPIP is standing for Epitope Presentation Integrated Prediction, a tool aims to find out tumor specific neoantigens

#Copyright (c) 2019, BGI-Shenzhen

EPIC version 1.0

Installation:

1. The software runs in the python3.x environment. Download the source code and decompress it, go into the decompressed directory and run the command bwlow:

pip install .

2. Make sure that PERL is installed and added to the PATH environmental vairable.

EPIP supports 3 modes by now:

1. mode1: predict epitope presentation based on PSSM only
2. mode2: predict epitope presentation using the full EPIP model, which integrates PSSM, peptide expression and length
3. mode3: add addition alleles to the EPIP supported allele repository. EPIP will build PSSM and obtain length distribution upon the provided peptide list and the corresponding allele.

Before using the software, try running the example codes below. Normally, running the codes should output nothing:

epip-predict -m 1 -l 9,10,11 -a HLA-A1101 -f EPIP/test/test_peptide.txt -o EPIP/test/my_test_peptide_mode1_A1101_myout.txt
diff EPIP/test/my_test_peptide_mode1_A1101_myout.txt EPIP/test/test_peptide_mode1_A1101_output.txt

epip-predict -m 2 -l 9,10,11 -a HLA-A1101 -f EPIP/test/test_peptide.txt -e EPIP/test/test_peptide_exp.txt -o EPIP/test/my_test_peptide_mode2_A1101_myout.txt\n
diff EPIP/test/my_test_peptide_mode2_A1101_myout.txt EPIP/test/test_peptide_mode2_A1101_output.txt

epip-predict -m 2 -l 9,10,11 -a HLA-B0801 -f EPIP/test/test_peptide.txt -e EPIP/test/test_peptide_exp.txt -o EPIP/test/my_test_peptide_mode2_B0801_myout.txt\n
diff EPIP/test/my_test_peptide_mode2_B0801_myout.txt EPIP/test/test_peptide_mode2_B0801_output.txt

Citation
If you find EPIP is useful to your research or work, please cite: Hu W, Qiu S, Li Y, et al. EPIC: MHC-I epitope prediction integrating mass spectrometry derived motifs and tissue-specific expression profiles[J]. bioRxiv, 2019: 567081.