ProteinGymR

Programmatic access to ProteinGym datasets in R/Bioconductor

Bioconductor version: 3.23 · Package version: 1.6.0

The ProteinGymR package provides analysis-ready data resources from ProteinGym, generated by Notin et al., 2023, as well as built-in functionality to visualize the data. ProteinGym comprises a collection of benchmarks for evaluating the performance of models predicting the effect of point mutations. This package provides access to 1. deep mutational scanning (DMS) scores from 217 assays measuring the impact of all possible amino acid substitutions across 186 proteins, 2. model performance metrics and prediction scores from 79 variant prediction models in the zero-shot setting and 12 models in the semi-supervised setting.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ProteinGymR")