Package: ClinicalVariantR 0.99.0

Safa Rafique

ClinicalVariantR: ACMG/AMP Germline Variant Interpretation from Annotated VCF Files

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.

Authors:Safa Rafique [aut, cre], Naeem Mahmood [aut], Muhammad Farooq Sabar [aut]

ClinicalVariantR_0.99.0.tar.gz
ClinicalVariantR_0.99.0.zip(r-4.7)ClinicalVariantR_0.99.0.zip(r-4.6)ClinicalVariantR_0.99.0.zip(r-4.5)
ClinicalVariantR_0.99.0.tgz(r-4.6-any)ClinicalVariantR_0.99.0.tgz(r-4.5-any)
ClinicalVariantR_0.99.0.tar.gz(r-4.7-any)ClinicalVariantR_0.99.0.tar.gz(r-4.6-any)
ClinicalVariantR_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ClinicalVariantR/json (API)

# Install 'ClinicalVariantR' in R:
install.packages('ClinicalVariantR', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/safarafique/clinicalvariantr/issues

On CRAN:

Conda:

softwarevariantannotationgeneticssequencingclassificationvisualizationgui

3.48 score 2 exports 111 dependencies

Last updated from:2c08894bfb. Checks:8 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING182
linux-devel-x86_64WARNING184
source / vignettesOK305
linux-release-x86_64WARNING188
macos-release-arm64WARNING128
macos-oldrel-arm64WARNING122
windows-develWARNING109
windows-releaseWARNING115
windows-oldrelWARNING132
wasm-releaseOK155

Exports:ClinicalVariantRClinicalVariantRApp

Dependencies:abindAnnotationDbiaskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebslibcachemcigarilloclicliprcodetoolscommonmarkcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestDTevaluatefastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgluehighrhmshtmltoolshtmlwidgetshttpuvhttrIRangesjquerylibjsonliteKEGGRESTknitrlambda.rlaterlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslotelpillarpkgconfigpngprettyunitsprogresspromisesR6rappdirsRcppRCurlreadrrestfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassSeqinfoshinysnowsourcetoolsSparseArraySummarizedExperimentsystibbletidyselecttinytextzdbutf8VariantAnnotationvctrsvroomwithrxfunXMLxtableXVectoryaml

Introduction to ClinicalVariantR
Overview | Installation | Launching the Shiny app | Input requirements | Scope and limitations | Session info
Rendered fromClinicalVariantR.Rmdusingknitr::rmarkdown

Last update: 2026-07-16
Started: 2026-07-16

Running and testing ClinicalVariantR
Purpose | Prerequisites | Launch the Shiny app | Preferred Bioconductor API | Source-tree launch (development) | Session settings useful for testing | Test data locations | Interactive testing checklist (UI) | Group B - Automated prediction (start here) | Group C - Gene panel | Group A - Full clinical | Automated testing (command line) | Unit tests (testthat) | Engine / pipeline scripts | Optional upload-flow smoke script | Optional Bioconductor / style checks (before submission) | Expected app object (non-interactive sanity check) | Troubleshooting while testing | Recommended smoke sequence (15 minutes) | Session info
Rendered fromClinicalVariantR-run-and-test.Rmdusingknitr::rmarkdown

Last update: 2026-07-16
Started: 2026-07-16

Readme and manuals

Help Manual

Help pageTopics
Build the ClinicalVariantR Shiny applicationClinicalVariantR ClinicalVariantRApp