Package: AlphaMissenseR
Title: Accessing AlphaMissense Data Resources in R
Version: 1.6.1
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",
        comment = c(ORCID = "0000-0003-4809-6227")
    ), 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 (>= 1.3.1), rlang, curl,
        BiocFileCache, spdl, memoise, BiocBaseUtils, utils, stats,
        tools, methods, whisker, ggplot2
Suggests: BiocManager, BiocGenerics, S4Vectors, Seqinfo, GenomeInfoDb,
        GenomicRanges, AnnotationHub, ExperimentHub, ensembldb, httr,
        tidyr, r3dmol, bio3d, shiny, shiny.gosling, ggdist, colorspace,
        knitr, rmarkdown, testthat (>= 3.0.0)
biocViews: SNP, Annotation, FunctionalGenomics, StructuralPrediction,
        Transcriptomics, VariantAnnotation, GenePrediction,
        ImmunoOncology
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/pak/sysreqs: libicu-dev libssl-dev xz-utils
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-11-26 19:34:30 UTC
RemoteUrl: https://github.com/bioc/AlphaMissenseR
RemoteRef: RELEASE_3_22
RemoteSha: 6684a18a067fc6c6b6def4d232550c9411caccf4
NeedsCompilation: no
Packaged: 2026-02-25 07:37:23 UTC; root
Author: Martin Morgan [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5874-8148>),
  Tram Nguyen [aut] (ORCID: <https://orcid.org/0000-0003-4809-6227>),
  Tyrone Lee [ctb],
  Nitesh Turaga [ctb],
  Chan Zuckerberg Initiative DAF CZF2019-002443 [fnd],
  NIH NCI ITCR U24CA180996 [fnd],
  NIH NCI IOTN U24CA232979 [fnd],
  NIH NCI ARTNet U24CA274159 [fnd]
Maintainer: Martin Morgan <mtmorgan.xyz@gmail.com>
Built: R 4.5.2; ; 2026-02-25 07:39:23 UTC; windows
