mhc-ii-pred

A model for predicting peptide to MHC type II binding.

How To Run

Just the Model

First install the dependencies required by the project:

pip install poetry
poetry install

To run the model run:

poetry run python -m mhc_ii_pred

To see the usage, you can either checkout run.py or run:

poetry run python -m mhc_ii_pred --help

Training on NetMHCIIPan Data

1. Install the dependencies as instructed by the previous section
2. Download that data from their website
3. Convert their data by running: poetry run python scripts/netmhc_to_json.py <extracted_data_dir>
4. Train the model by running: poetry run python -m mhc_ii_pred train output_EL.json