Package: ProteinGymR
Title: Programmatic access to ProteinGym datasets in R/Bioconductor
Version: 1.7.0
Authors@R: 
    c(person("Tram", "Nguyen",
            role = c("aut", "cre"),
            email = "tram22.nguyen@gmail.com",
            comment = c(ORCID = "0000-0003-4809-6227")),
      person("Pascal", "Notin", 
            role = "aut"),
      person("Aaron", "Kollasch", 
            role = "aut"),
      person("Debora", "Marks", 
            role = "aut"),
      person("Ludwig", "Geistlinger", 
            role = "aut"))
Description: 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.
License: Artistic-2.0
URL: https://github.com/ccb-hms/ProteinGymR
BugReports: https://github.com/ccb-hms/ProteinGymR/issues
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)
VignetteBuilder: knitr
Encoding: UTF-8
biocViews: ExperimentData, ExperimentHub, PackageTypeData,
        Homo_sapiens_Data, ReproducibleResearch, CellCulture,
        SequencingData, Proteome
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Config/testthat/edition: 3
Config/pak/sysreqs: libicu-dev libpng-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:37:44 UTC
RemoteUrl: https://github.com/bioc/ProteinGymR
RemoteRef: HEAD
RemoteSha: c3b8833ed0775ea2f82d2898d980c11561a1b21c
NeedsCompilation: no
Packaged: 2026-10-10 10:47:50 UTC; root
Author: Tram Nguyen [aut, cre] (ORCID: <https://orcid.org/0000-0003-4809-6227>),
  Pascal Notin [aut],
  Aaron Kollasch [aut],
  Debora Marks [aut],
  Ludwig Geistlinger [aut]
Maintainer: Tram Nguyen <tram22.nguyen@gmail.com>