Git Product home page Git Product logo

epic's Introduction

EPIC

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:

  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 .

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

EPIC supports 3 modes by now:

  1. mode1: predict epitope presentation based on PSSM only
  2. mode2: predict epitope presentation using the full EPIC model, which integrates PSSM, peptide expression and length
  3. 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

epic's People

Contributors

bgi2016 avatar weipeneghu avatar

Watchers

 avatar  avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.