DOI: 10.18129/B9.bioc.VarCon  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see VarCon.

VarCon: an R package for retrieving neighboring nucleotides of an SNV

Bioconductor version: 3.16

VarCon is an R package which converts the positional information from the annotation of an single nucleotide variation (SNV) (either referring to the coding sequence or the reference genomic sequence). It retrieves the genomic reference sequence around the position of the single nucleotide variation. To asses, whether the SNV could potentially influence binding of splicing regulatory proteins VarCon calcualtes the HEXplorer score as an estimation. Besides, VarCon additionally reports splice site strengths of splice sites within the retrieved genomic sequence and any changes due to the SNV.

Author: Johannes Ptok [aut, cre]

Maintainer: Johannes Ptok <Johannes.Ptok at>

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biocViews AlternativeSplicing, FunctionalGenomics, Software
Version 1.6.0
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License GPL-3
Depends Biostrings, BSgenome, GenomicRanges, R (>= 4.1)
Imports methods, stats, IRanges, shiny, shinycssloaders, shinyFiles, ggplot2
Suggests testthat, knitr, rmarkdown
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