G4SNVHunter
This is the development version of G4SNVHunter; for the stable release version, see G4SNVHunter.
Evaluating SNV-Induced Disruption of G-Quadruplex Structures
Bioconductor version: Development (3.22)
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 propensity and to accurately screen user-provided single nucleotide variants—as well as other small-scale variants such as indels and MNVs—for their potential to destabilize these structures. This allows researchers to then screen these critical variants for deeper study, digging into how they might influence biological functions—think gene regulation, for instance—by impairing G4 formation propensity.
Author: Rongxin Zhang [cre, aut]
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 | 1.1.4 |
| In Bioconductor since | BioC 3.21 (R-4.5) (< 6 months) |
| 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, tools, SummarizedExperiment, VariantAnnotation, dplyr, openxlsx, tidyr, magrittr, ggdensity |
| 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_1.1.4.tar.gz |
| Windows Binary (x86_64) | G4SNVHunter_1.1.4.zip |
| macOS Binary (x86_64) | G4SNVHunter_1.1.4.tgz |
| macOS Binary (arm64) | G4SNVHunter_1.1.4.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 |