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This is the development version of VarCon; for the stable release version, see VarCon.

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

Bioconductor version: Development (3.20)

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>

Citation (from within R, enter citation("VarCon")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Analysing SNVs with VarCon HTML R Script
Reference Manual PDF


biocViews AlternativeSplicing, FunctionalGenomics, Software
Version 1.13.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-3
Depends Biostrings, BSgenome, GenomicRanges, R (>= 4.1)
Imports methods, stats, IRanges, shiny, shinycssloaders, shinyFiles, ggplot2
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Suggests testthat, knitr, rmarkdown
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Follow Installation instructions to use this package in your R session.

Source Package VarCon_1.13.0.tar.gz
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macOS Binary (x86_64) VarCon_1.13.0.tgz
macOS Binary (arm64) VarCon_1.13.0.tgz
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Source Repository (Developer Access) git clone
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