epitopes package

Processing, Feature Extraction and modelling of epitope data from the Immune Epitope Database (IEDB)

Authors:

• Felipe Campelo - f.campelo@aston.ac.uk, fcampelo@gmail.com
• Jodie Ashford - ashfojsm@aston.ac.uk

Contributors:

• Francisco Lobo - franciscolobo@ufmg.br
• Joao Reis-Cunha - jaumlrc@gmail.com

Current version:

• 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.

Upcoming:

• Plotting functions

Usage

Check Vignette Usage example for a quick tutorial.

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Please report any bugs or suggestions directly in the repository Issues page.