Package: rvarsim 0.99.1

Liu Sun

rvarsim: R/Bioconductor Variant Simulator with HGVS Notation

Simulates all possible single nucleotide variants (SNVs) across MANE Select transcripts including coding sequence (CDS), untranslated regions (UTRs), and canonical splice sites. Outputs variants in HGVS notation. Provides a comprehensive HGVS toolkit: parsing, syntactic and semantic validation, normalization (3' shifting, common affix trimming), format conversion (HGVS <-> VCF <-> SPDI), transcription mapping (genomic <-> coding), translation to protein consequence, backtranslation from protein to coding variants, variant extraction from sequence alignment, and liftover between genome assemblies.

Authors:Liu Sun [aut, cre]

rvarsim_0.99.1.tar.gz
rvarsim_0.99.1.zip(r-4.7)rvarsim_0.99.1.zip(r-4.6)rvarsim_0.99.1.zip(r-4.5)
rvarsim_0.99.1.tgz(r-4.6-any)rvarsim_0.99.1.tgz(r-4.5-any)
rvarsim_0.99.1.tar.gz(r-4.7-any)rvarsim_0.99.1.tar.gz(r-4.6-any)
rvarsim_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
rvarsim/json (API)

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

Bug tracker:https://github.com/liu-sun/rvarsim/issues

On CRAN:

Conda:

geneticsvariantannotationsnpsequencingtranscriptionvariantdetectionalignmentnormalization

2.70 score 21 exports 74 dependencies

Last updated from:7b0d289ded. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE303
linux-devel-x86_64NOTE496
source / vignettesOK371
linux-release-x86_64NOTE447
macos-release-arm64NOTE283
macos-oldrel-arm64NOTE388
windows-develNOTE377
windows-releaseNOTE371
windows-oldrelNOTE387
wasm-releaseOK266

Exports:backtranslate_hgvsc_to_gextract_hgvsfetch_mane_txdbformat_hgvsg_to_cgenerate_variantsget_transcript_structurehgvs_to_spdihgvs_to_vcfis_valid_hgvsliftover_c_hgvsliftover_hgvsnormalize_hgvsparse_hgvssimulate_variantsspdi_to_hgvstranscribe_hgvstranslate_hgvsvalidate_hgvsvcf_to_hgvs

Dependencies:abindAnnotationDbiAnnotationFilteraskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayensembldbfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelazyevallifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngProtGenericsR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryaml

rvarsim: Variant Simulation with HGVS Notation

Liu Sun

Rendered fromrvarsim.Rmdusingknitr::rmarkdownon Jun 10 2026.

Last update: 2026-06-10
Started: 2026-06-10