Processing, Feature Extraction and modelling of epitope data from the Immune Epitope Database (IEDB)
- Felipe Campelo - f.campelo@aston.ac.uk, fcampelo@gmail.com
- Jodie Ashford - ashfojsm@aston.ac.uk
- Francisco Lobo - franciscolobo@ufmg.br
- Joao Reis-Cunha - jaumlrc@gmail.com
- Consolidation of linear B-cell epitopes from the full IEDB database and retrieval of protein data from NBCI and Uniprot.
- Organism- and taxon-based filtering of epitope data.
- Data splitting for machine learning based on protein dissimilarity.
- Extraction of observations for feature calculation using a sliding window representation.
- Calculation of sequence-based features.
- Read prediction output from other predictors (ABCPred, Bepipred 2.0, iBCE-EL, LBtope, SVMTrip)
- Fitting classification models to data with hold-out set-based assessment.
- Plotting functions
Check Vignette Usage example for a quick tutorial.
Please report any bugs or suggestions directly in the repository Issues page.