fcampelo / OrgSpec-paper

Full reproducibility scripts and data for paper "Organism Specific Data Sets Improve Linear B-Cell Epitope Prediction Performance"

OrgSpec paper

Full reproducibility scripts and data for the paper "Organism Specific Data Sets Improve Linear B-Cell Epitope Prediction Performance".

The scripts contained in this folder make use of the epitopes package, version 0.5.1, which can be installed into R using:

devtools::install_github("fcampelo/epitopes", ref = "v0.5.1-OrgSpec-paper")

Our results were generated with the following setup (taking advantage of some parallel processing capabilities of the epitopes package):

R version 4.0.5 (2021-03-31)

Platform: x86_64-apple-darwin17.0 (64-bit)

Running under: macOS Big Sur 10.16

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How to re-run the experiment:

• Download or clone this repository locally.
• For each pathogen:
  1. Set the target organism folder (under directory Experiments) as the working directory.
  2. Execute routine 01_generate_datasets
  3. Generate predictions using the benchmark predictors (ABCPred, Bepipred2, etc.) for the hold-out proteins (under subfolder data/splits of your working directory) and save them to the appropriate folders under subfolder output.
• Run routine Check_leakage (under Experiments).
• For each pathogen:
  1. Execute routine 02_run_experiment
• Run routine Consolidate_results (under Experiments).

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