This repository contains the source code and data used for the manuscript "Estimating the Limits of Organism-Specific Training for Epitope Prediction", by J. Ashford, A. Ekárt and F. Campelo.
Notes:
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The data generation, modelling, analysis and plotting routines are under
/code. All steps except modelling were implemented in R; modelling was done in Python (scripts and environment under/code/02_modelling/). -
All data is located under
/data, including:- the base data for each organism (
01_training.rdsand02_holdout.rds) - heterogeneous data for each organism (
df_heterogeneous.rds) - baseline performance estimates extracted from https://academic.oup.com/bioinformatics/article/37/24/4826/6325084 (
analysis.rds) - results for each organism (
/data/Results/...). The .CSV files containing the resulting predictions have been compressed to comply with Github's file and repository size limits. Please expand these files prior to running the scripts in/code.
- the base data for each organism (
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Output files and summary tables of calculated performance metrics for all predictors are under
/outputs
If there are any queries, please contact me at f.campelo@aston.ac.uk or fcampelo@gmail.com.