https://github.com/fcampelo/epitopes2

Secret sauce for our epitope prediction and optimisation pipelines
https://github.com/fcampelo/epitopes2

Last synced: 4 days ago
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Secret sauce for our epitope prediction and optimisation pipelines

• Host: GitHub
• URL: https://github.com/fcampelo/epitopes2
• Owner: fcampelo
• Created: 2023-04-10T10:31:32.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2026-06-20T15:33:59.000Z (14 days ago)
• Last Synced: 2026-06-20T16:21:09.689Z (14 days ago)
• Language: R
• Size: 371 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS.md

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README

          
# epitopes package

  [![R-CMD-check](https://github.com/fcampelo/epitopes/workflows/R-CMD-check/badge.svg)](https://github.com/fcampelo/epitopes/actions)

  

Processing, Feature Extraction and modelling of epitope data from the Immune Epitope Database ([IEDB](http://iedb.org))

## Authors: 

- Felipe Campelo - [f.campelo@aston.ac.uk](mailto:f.campelo@aston.ac.uk), [fcampelo@gmail.com](mailto:fcampelo@gmail.com)

## Collaborators:

- Francisco Lobo - [franciscolobo@ufmg.br](mailto:franciscolobo@ufmg.br)

## Previous contributors:

- Jodie Ashford - [ashfojsm@aston.ac.uk](mailto:ashfojsm@aston.ac.uk)

- Joao Reis-Cunha - [jaumlrc@gmail.com](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](https://fcampelo.github.io/epitopes/articles/Usage-example.html) for a quick tutorial.

***

Please report any bugs or suggestions directly in the repository [Issues](https://github.com/fcampelo/epitopes/issues) page.