ProteinGymR
This is the released version of ProteinGymR; for the devel version, see ProteinGymR.
All Bioconductor versions of ProteinGymR
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20
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.
Author: Tram Nguyen [aut, cre] 
, Pascal Notin [aut], Aaron Kollasch [aut], Debora Marks [aut], Ludwig Geistlinger [aut]
Maintainer: Tram Nguyen <tram22.nguyen at gmail.com>
Citation
From within R, enter citation("ProteinGymR"):
Tram Nguyen, Pascal Notin, Aaron Kollasch, Debora Marks, Ludwig Geistlinger. ProteinGymR: Programmatic access to ProteinGym datasets in R/Bioconductor. doi:10.18129/B9.bioc.ProteinGymR, R package version 1.6.0, https://bioconductor.org/packages/ProteinGymR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ProteinGymR")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.6.0 |
| License | Artistic-2.0 |
| URL | https://github.com/ccb-hms/ProteinGymR |
| Bug Reports | https://github.com/ccb-hms/ProteinGymR/issues |
| Last updated | 2026-05-05 |
| In Bioconductor since | BioC 3.20 (R-4.4) (1 year) |
| Downloads rank | 386 of 434 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | CellCulture, ExperimentData, ExperimentHub, Homo_sapiens_Data, PackageTypeData, Proteome, ReproducibleResearch, SequencingData |
| Package Short Url | https://bioconductor.org/packages/ProteinGymR/ |
Documentation
| Reference Manual |
Download
Follow the installation instructions to use this package in your R session.
| Source package | ProteinGymR_1.6.0.tar.gz |
| Source Repository | git clone https://git.bioconductor.org/packages/ProteinGymR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ProteinGymR |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.4.0)
Imports: ExperimentHub, AnnotationHub, dplyr, purrr, queryup, spdl, tidyr, tidyselect, stringr, lifecycle, rlang, htmltools
Suggests: tibble, BiocStyle, knitr, testthat (>= 3.0.0), ComplexHeatmap, circlize, pals, ggplot2 (>= 3.5.0), grDevices, ggExtra, bio3d, r3dmol, forcats, ggdist (>= 3.3.0)