G4SNVHunter
This is the development version of G4SNVHunter; to use it, please install the devel version of Bioconductor.
Evaluating SNV-Induced Disruption of G-Quadruplex Structures
Bioconductor version: Development (3.21)
G-quadruplexes (G4s) are unique nucleic acid secondary structures predominantly found in guanine-rich regions and have been shown to be involved in various biological regulatory processes. G4SNVHunter is an R package designed to rapidly identify genomic sequences with G4-forming potential and accurately screen user-provided single nucleotide variants (also applicable to single nucleotide polymorphisms) that may destabilize these structures. This enables users to screen key variants for further experimental study, investigating how these variants may influence biological functions, such as gene regulation, by altering G4 formation.
Author: Rongxin Zhang [cre, aut] (ORCID:
Maintainer: Rongxin Zhang <rongxinzhang at outlook.com>
citation("G4SNVHunter")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("G4SNVHunter")
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("G4SNVHunter")| Introduction to G4SNVHunter | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Epigenetics, SNP, Software |
| Version | 0.99.4 |
| In Bioconductor since | BioC 3.21 (R-4.5) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.3.0) |
| Imports | Biostrings, stats, GenomicRanges, IRanges, Rcpp, RcppRoll, data.table, GenomeInfoDb, S4Vectors, ggplot2, cowplot, progress, ggseqlogo, viridis, ggpointdensity |
| System Requirements | |
| URL | https://github.com/rongxinzh/G4SNVHunter |
| Bug Reports | https://github.com/rongxinzh/G4SNVHunter/issues |
See More
| Suggests | knitr, BiocStyle, rmarkdown, BiocManager, BSgenome.Hsapiens.UCSC.hg19, DT, rtracklayer, testthat (>= 3.0.0), RBGL |
| Linking To | Rcpp |
| 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 | G4SNVHunter_0.99.4.tar.gz |
| Windows Binary (x86_64) | G4SNVHunter_0.99.4.zip |
| macOS Binary (x86_64) | G4SNVHunter_0.99.4.tgz |
| macOS Binary (arm64) | G4SNVHunter_0.99.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/G4SNVHunter |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/G4SNVHunter |
| Bioc Package Browser | https://code.bioconductor.org/browse/G4SNVHunter/ |
| Package Short Url | https://bioconductor.org/packages/G4SNVHunter/ |
| Package Downloads Report | Download Stats |