ClinicalVariantR is an R / Bioconductor software package that classifies germline sequence variants under the ACMG/AMP 2015 framework from pre-annotated VCF files (VEP CSQ, SnpEff ANN, or ANNOVAR-style INFO fields).
The package exposes an interactive Shiny application with three workflows:
| Workflow | Inputs | Purpose |
|---|---|---|
| Group A (full clinical) | VCF + clinical log + pedigree | Automated criteria plus curator toggles |
| Group B (rapid) | VCF only | High-throughput automated classification |
| Group C (gene panel) | VCF + gene list | Panel-restricted automated classification |
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("ClinicalVariantR")Until the package is accepted on Bioconductor, install from GitHub:
Following Bioconductor Shiny guidelines, package functions return a Shiny app object; the user launches it:
if (requireNamespace("ClinicalVariantR", quietly = TRUE)) {
stopifnot(is.function(ClinicalVariantR::ClinicalVariantR))
}
# To launch interactively:
# shiny::runApp(ClinicalVariantR())ClinicalVariantRApp() is an alias of
ClinicalVariantR().
For a full walkthrough of launching the app, choosing sample VCFs,
Group A/B/C UI checks, and command-line tests, see the companion
vignette Running and testing ClinicalVariantR
(vignettes/ClinicalVariantR-run-and-test.Rmd).
.vcf or .vcf.gz)
with VEP CSQ, SnpEff ANN, or ANNOVAR-style
annotation for consequence, gene symbol, transcript, population AF,
ClinVar, and in silico scores when available.Default reference tables under inst/extdata/reference/
are placeholders; population and prediction evidence primarily use
annotation embedded in the VCF unless curated references are installed
(see package README).
ClinicalVariantR targets germline SNV and small-indel interpretation. It does not classify somatic variants, structural variants, CNVs, or mitochondrial genomes. Several ACMG criteria require external data (functional assays, phasing, matched pathogenic variants) and are registered as manual or not automated.
See the package NEWS file and GitHub README for
version-specific criterion coverage and validation notes.
sessionInfo()
#> R version 4.6.1 (2026-06-24)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 26.04 LTS
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#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] BiocStyle_2.41.0
#>
#> loaded via a namespace (and not attached):
#> [1] cli_3.6.6 knitr_1.51 rlang_1.3.0
#> [4] xfun_0.60 otel_0.2.0 promises_1.5.0
#> [7] shiny_1.14.0 xtable_1.8-8 jsonlite_2.0.0
#> [10] buildtools_1.0.0 htmltools_0.5.9 maketools_1.3.2
#> [13] httpuv_1.6.17 sys_3.4.3 sass_0.4.10
#> [16] rmarkdown_2.31 evaluate_1.0.5 jquerylib_0.1.4
#> [19] fastmap_1.2.0 yaml_2.3.12 lifecycle_1.0.5
#> [22] ClinicalVariantR_0.99.0 BiocManager_1.30.27 compiler_4.6.1
#> [25] Rcpp_1.1.2 later_1.4.8 digest_0.6.39
#> [28] R6_2.6.1 magrittr_2.0.5 bslib_0.11.0
#> [31] tools_4.6.1 mime_0.13 cachem_1.1.0