Bioconductor - VarCon

This is the released version of VarCon; for the devel version, see VarCon.

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

Bioconductor version: Release (3.22)

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 posteo.de>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("VarCon")

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

Documentation

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

browseVignettes("VarCon")

Details

biocViews	AlternativeSplicing, FunctionalGenomics, Software
Version	1.18.0
In Bioconductor since	BioC 3.13 (R-4.1) (5 years)
License	GPL-3
Depends	Biostrings, BSgenome, GenomicRanges, R (>= 4.1)
Imports	methods, stats, IRanges, shiny, shinycssloaders, shinyFiles, ggplot2
System Requirements
URL

Package Archives

Follow Installation instructions to use this package in your R session.