DESCRIPTION

Package: ProteinGymR
Title: Programmatic access to ProteinGym datasets in R/Bioconductor
Version: 1.3.0
Authors@R: 
    c(person("Tram", "Nguyen",
            role = c("aut", "cre"),
            email = "Tram_Nguyen@hms.harvard.edu",
            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,
    bio3d,
    r3dmol,
    ggExtra,
    dplyr,
    forcats,
    ggdist,
    gghalves,
    ggplot2,
    purrr,
    queryup,
    spdl,
    tidyr,
    tidyselect,
    ComplexHeatmap,
    circlize,
    stringr
Suggests: 
    tibble,
    BiocStyle,
    knitr,
    testthat (>= 3.0.0)
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