EPIC 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:
- 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 .
- Make sure that PERL is installed and added to the PATH environmental vairable.
EPIC supports 3 modes by now:
- mode1: predict epitope presentation based on PSSM only
- mode2: predict epitope presentation using the full EPIC model, which integrates PSSM, peptide expression and length
- mode3: add addition alleles to the EPIC supported allele repository. EPIC 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:
epic-predict -m 1 -l 9,10,11 -a HLA-A1101 -f EPIC/test/test_peptide.txt -o EPIC/test/my_test_peptide_mode1_A1101_myout.txt
diff EPIC/test/my_test_peptide_mode1_A1101_myout.txt EPIC/test/test_peptide_mode1_A1101_output.txt
epic-predict -m 2 -l 9,10,11 -a HLA-A1101 -f EPIC/test/test_peptide.txt -e EPIC/test/test_peptide_exp.txt -o EPIC/test/my_test_peptide_mode2_A1101_myout.txt\n
diff EPIC/test/my_test_peptide_mode2_A1101_myout.txt EPIC/test/test_peptide_mode2_A1101_output.txt
epic-predict -m 2 -l 9,10,11 -a HLA-B0801 -f EPIC/test/test_peptide.txt -e EPIC/test/test_peptide_exp.txt -o EPIC/test/my_test_peptide_mode2_B0801_myout.txt\n
diff EPIC/test/my_test_peptide_mode2_B0801_myout.txt EPIC/test/test_peptide_mode2_B0801_output.txt
Citation
If you find EPIC is useful to your research or work, please cite