ashrosewood / DeepImmuno

Deep-learning empowered prediction and generation of immunogenic epitopes for T cell immunity

DeepImmuno

Deep-learning empowered prediction and generation of immunogenic epitopes for T cell immunity.

We recommend to try out our web application for that: https://deepimmuno.research.cchmc.org

The repository for building the DeepImmuno web server: https://github.com/frankligy/DeepImmuno-web

• Please refer to DeepImmuno-CNN if you want to predict immunogenicity

• Please refer to DeepImmuno-GAN if you want to generate immunogenic peptide

• Please refer to Train your own GAN if you want to generate peptides with customized features/properties.

Enjoy and don't hesitate to ask me questions (contact at the bottom), I will be responsive! Feel free to raise an issue on github page!

Citation

If you find that tool useful in your research, please consider citing our paper:

DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity, Briefings in Bioinformatics, May 03 2021 (https://doi.org/10.1093/bib/bbab160)

Reproduce

All the codes for reproducing figures in the manucript can be accessed in /reproduce/fig

FAQ

1. Why I get zero immunogenicity score when running on deepimmno webserver?

Currently, Deepimmuno-CNN only supports peptides in the length of 9 and 10. We are working on adding support to peptides of other length and it will be available in the future version. But for now, it is advisable to filter to your queried peptides to 9mer and 10mer.

2. How did I obtain the paratope information to encode the HLA?

I compile a README.md file for all the detailed steps, feel free to contact me if you have any confusions.

DeepImmuno-CNN

Dependencies

python = 3.6

tensorflow = 2.3.0

numpy = 1.18.5

pandas = 1.1.1

• Note: This is the enviroment that I used for development and I also tested it. But as long as you use python > 3, tensorflow = 2.3, It should also work.

How to use?

If you want to query a single epitope (peptide + HLA), for example you want to query peptide HPPLMNVER along with HLA-A*0201. You need to

python3 deepimmuno-cnn.py --mode "single" --epitope "HPPLMNVER" --hla "HLA-A*0201"

If you want to query multiple epitopes, you just need to prepare a csv file like this:

AAAAAAAAA,HLA-A*0201
CCCCCCCCC,HLA-B*5801
DDDDDDDDD,HLA-C*0702

Then you run:

python3 deepimmuno-cnn.py --mode "multiple" --intdir "/path/to/above/file" --outdir "/path/to/output/folder"

• Please note, when you specify the output dir, don't include the forward slash at the end, for example, use "/Desktop" instead "/Desktop/"

• PLease note, if python3 doesn't work, you can replace python3 to python, it depends your installed python interpreter

A full help prompt is as below:

usage: deepimmuno-cnn.py [-h] [--mode MODE] [--epitope EPITOPE] [--hla HLA]
                         [--intdir INTDIR] [--outdir OUTDIR]

DeepImmuno-CNN command line

optional arguments:
  -h, --help         show this help message and exit
  --mode MODE        single mode or multiple mode
  --epitope EPITOPE  if single mode, specifying your epitope
  --hla HLA          if single mode, specifying your HLA allele
  --intdir INTDIR    if multiple mode, specifying the path to your input file
  --outdir OUTDIR    if multiple mode, specifying the path to your output folder

DeepImmuno-GAN

Dependencies

python = 3.6

pytorch = 1.4.0

numpy = 1.18.4

pandas = 1.0.5

• Note: This is the enviroment that I used for development and I also tested it. But as long as you use python > 3, pytorch = 1.4, It should also work.

How to use

Pretty simple, just run like this

python3 deepimmuno-gan.py --outdir "/path/to/store/output"

It will automatically genearte one batch, which is 64 pseudo-immunogenic peptides of HLA-A*0201 for your. It is worth noting that, because of the way I encode the peptide, there will be a placeholder "-".

A full help prompt is as below

usage: deepimmuno-gan.py [-h] [--outdir OUTDIR]

DeepImmuno-GAN to generate immunogenic peptide

optional arguments:
  -h, --help       show this help message and exit
  --outdir OUTDIR  specifying your output folder

• Please note, when you specify the output dir, don't include the forward slash at the end, for example, use "/Desktop" instead "/Desktop/"

• PLease note, if python3 doesn't work, you can replace python3 to python, it depends your installed python interpreter

Contact

Guangyuan(Frank) Li

[e-mail]

PhD student, Biomedical Informatics

Cincinnati Children's Hospital Medical Center(CCHMC)

University of Cincinnati, College of Medicine