Package: ClinicalVariantR
Title: ACMG/AMP Germline Variant Interpretation from Annotated VCF
        Files
Version: 0.99.0
Date: 2026-07-08
Authors@R: c(
    person(
        given = "Safa",
        family = "Rafique",
        email = "safa.sandhu@gmail.com",
        role = c("aut", "cre"),
        comment = c(ORCID = "0000-0003-2646-8106")
    ),
    person(
        given = "Naeem",
        family = "Mahmood",
        email = "naeem.sbb@pu.edu.pk",
        role = "aut"
    ),
    person(
        given = "Muhammad Farooq",
        family = "Sabar",
        email = "farooq.sbb@pu.edu.pk",
        role = "aut"
    )
    )
Author: Safa Rafique [aut, cre] (ORCID: 0000-0003-2646-8106), Naeem
        Mahmood [aut], Muhammad Farooq Sabar [aut]
Maintainer: Safa Rafique <safa.sandhu@gmail.com>
Description: ClinicalVariantR is an interactive Shiny platform for
        evidence-based germline variant classification under ACMG/AMP
        2015 guidelines. It accepts VEP-, SnpEff-, or ANNOVAR-annotated
        VCF files, applies automated and curator-guided ACMG criteria,
        supports streaming analysis of large call sets, and exports
        structured per-criterion evidence with reproducibility
        metadata.
License: MIT + file LICENSE
URL: https://github.com/safarafique/ClinicalVariantR
BugReports: https://github.com/safarafique/ClinicalVariantR/issues
biocViews: Software, VariantAnnotation, Genetics, Sequencing,
        Classification, Visualization, GUI
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Depends: R (>= 4.5.0)
Imports: shiny (>= 1.8.0), bslib, DT, data.table, readr, jsonlite,
        VariantAnnotation, methods, stats, utils
Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), BiocCheck,
        shinytest2
Config/testthat/edition: 3
Config/Needs/website: BiocStyle
SystemRequirements: Optional: bcftools for accelerated VCF streaming on
        Linux/WSL.
Config/pak/sysreqs: cmake make libbz2-dev liblzma-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev libx11-dev xz-utils
        zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-07-16 09:40:22 UTC
RemoteUrl: https://github.com/BiocStaging/ClinicalVariantR
RemoteRef: HEAD
RemoteSha: 2c08894bfba4c5dd5aa1f1e066898d62a9918a13
NeedsCompilation: no
Packaged: 2026-07-16 20:40:23 UTC; root