VarCon
This package is for version 3.17 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: 3.17
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("VarCon")):
Installation
To install this package, start R (version "4.3") 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")| Analysing SNVs with VarCon | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | AlternativeSplicing, FunctionalGenomics, Software |
| Version | 1.8.0 |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | testthat, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | VarCon_1.8.0.tar.gz |
| Windows Binary | VarCon_1.8.0.zip |
| macOS Binary (x86_64) | VarCon_1.8.0.tgz |
| macOS Binary (arm64) | VarCon_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/VarCon |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/VarCon |
| Bioc Package Browser | https://code.bioconductor.org/browse/VarCon/ |
| Package Short Url | https://bioconductor.org/packages/VarCon/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.17 | Source Archive |