VarCon

DOI: 10.18129/B9.bioc.VarCon    

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 (3.15)

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>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.3.0
In Bioconductor since BioC 3.13 (R-4.1) (0.5 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
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package VarCon_1.3.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) VarCon_1.3.0.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

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