Package: ClinicalVariantR
Title: Clinical Variant Interpretation Using ACMG/AMP Germline Criteria
Version: 0.99.3
Date: 2026-07-22
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"
    )
    )
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 and applies automated plus curator-guided ACMG
        criteria. The package supports streaming analysis of large call
        sets and exports structured per-criterion evidence with
        reproducibility metadata for clinical review.
License: MIT + file LICENSE
URL: https://github.com/safarafique/ClinicalVariantR
BugReports: https://github.com/safarafique/ClinicalVariantR/issues
biocViews: Software, VariantAnnotation, Genetics, Sequencing,
        Visualization, GUI, Classification
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 8.0.0
VignetteBuilder: knitr
Depends: R (>= 4.5.0)
Imports: shiny (>= 1.8.0), bslib, DT, data.table, digest, readr,
        jsonlite, methods, openssl, stats, utils, VariantAnnotation
Suggests: BiocStyle, knitr, rmarkdown, ggplot2, shinyjs, 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: 2026-07-31 05:59:19 UTC
RemoteUrl: https://github.com/BiocStaging/ClinicalVariantR
RemoteRef: HEAD
RemoteSha: 72cd727e3f1e64ca699d8c6630e2ff91c01fe78d
NeedsCompilation: no
Packaged: 2026-09-30 09:33:36 UTC; root
Author: Safa Rafique [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-2646-8106>),
  Naeem Mahmood [aut],
  Muhammad Farooq Sabar [aut]