VarCon

DOI: 10.18129/B9.bioc.VarCon    

This package is for version 3.15 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: 3.15

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Analysing SNVs with VarCon
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	AlternativeSplicing, FunctionalGenomics, Software
Version	1.4.0
In Bioconductor since	BioC 3.13 (R-4.1) (1.5 years)
License	GPL-3
Depends	Biostrings, BSgenome, GenomicRanges, R (>= 4.1)
Imports	methods, stats, IRanges, shiny, shinycssloaders, shinyFiles, ggplot2
LinkingTo
Suggests	testthat, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
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Build Report

Package Archives

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

Source Package	VarCon_1.4.0.tar.gz
Windows Binary	VarCon_1.4.0.zip
macOS Binary (x86_64)	VarCon_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/VarCon
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/VarCon
Package Short Url	https://bioconductor.org/packages/VarCon/
Package Downloads Report	Download Stats