DESCRIPTION

Package: AlphaMissenseR
Title: Accessing AlphaMissense Data Resources in R
Version: 1.1.7
Authors@R:
    c(person(
        "Martin", "Morgan", role = c("aut", "cre"),
        email = "mtmorgan.xyz@gmail.com",
        comment = c(ORCID = "0000-0002-5874-8148")
    ), person(
        "Tram", "Nguyen",
        role = "aut"
    ), person(
        "Tyrone", "Lee",
        role = "ctb"
    ), person(
        "Nitesh", "Turaga",
        role = "ctb"
    ), person(
        "Chan Zuckerberg Initiative DAF CZF2019-002443",
        role = "fnd"
    ), person(
        "NIH NCI ITCR U24CA180996",
        role = "fnd"
    ), person(
        "NIH NCI IOTN U24CA232979",
        role = "fnd"
    ), person(
        "NIH NCI ARTNet U24CA274159",
        role = "fnd"
    ))
Description:
    The AlphaMissense publication
    <https://www.science.org/doi/epdf/10.1126/science.adg7492>
    outlines how a variant of AlphaFold / DeepMind was used to predict
    missense variant pathogenicity. Supporting data on Zenodo
    <https://zenodo.org/record/10813168> include, for instance, 71M
    variants across hg19 and hg38 genome builds. The 'AlphaMissenseR'
    package allows ready access to the data, downloading individual
    files to DuckDB databases for exploration and integration into *R*
    and *Bioconductor* workflows.
License: Artistic-2.0
URL: https://mtmorgan.github.io/AlphaMissenseR/
BugReports: https://github.com/mtmorgan/AlphaMissenseR/issues
Depends:
    R (>= 4.3.0),
    dplyr
Imports:
    rjsoncons (>= 1.0.1), DBI, duckdb (>= 0.9.1), rlang,
    curl, BiocFileCache, spdl, memoise, BiocBaseUtils,
    utils, stats, tools, methods, whisker, ggplot2
Suggests:
    BiocManager,
    BiocGenerics,
    GenomicRanges,
    GenomeInfoDb,
    AnnotationHub,
    ExperimentHub,
    ensembldb,
    httr,
    tidyr,
    r3dmol, bio3d, shiny, shiny.gosling,
    ggdist, gghalves,
    colorspace,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
biocViews: SNP, Annotation, FunctionalGenomics, StructuralPrediction,
    Transcriptomics, VariantAnnotation, GenePrediction, ImmunoOncology
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Config/testthat/edition: 3