Pipeline for DePTH

code_for_data

Code files for processing Emerson data and generating TCR-HLA pairs used for developing DePTH models, processing Zheng 2021 single cell potentially cancer-related TCRs, preparing pairs based on Szeto 2020 solved structures and, and preparing McPAS files for DePTH McPAS.

cv_train_predict

Bash scripts to do cross-validation, train DePTH models and make predictions, and code files to average predicted scores from 20 models (trained using 20 different sets of random seeds) in each setting. Code in this folder should be run on the same level as data and results folders. They are put in cv_train_predict folder only for the purpose of organization.

code_for_results

Code files for generating results based on predicted scores.

code_for_draft

Code files for generating figures used in paper draft.