pqsfinder

DOI: 10.18129/B9.bioc.pqsfinder  

Identification of potential quadruplex forming sequences

Bioconductor version: Release (3.16)

Pqsfinder detects DNA and RNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, pqsfinder is able to detect G4s folded from imperfect G-runs containing bulges or mismatches or G4s having long loops. Pqsfinder also assigns an integer score to each hit that was fitted on G4 sequencing data and corresponds to expected stability of the folded G4.

Author: Jiri Hon, Dominika Labudova, Matej Lexa and Tomas Martinek

Maintainer: Jiri Hon <jiri.hon at gmail.com>

Installation

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

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

BiocManager::install("pqsfinder")

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("pqsfinder")

 

HTML	R Script	pqsfinder: User Guide
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GeneRegulation, MotifDiscovery, SequenceMatching, Software
Version	2.14.1
In Bioconductor since	BioC 3.3 (R-3.3) (7 years)
License	BSD_2_clause + file LICENSE
Depends	R (>= 3.5.0), Biostrings
Imports	Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods
LinkingTo	Rcpp, BH (>= 1.78.0)
Suggests	BiocStyle, knitr, rmarkdown, Gviz, rtracklayer, ggplot2, BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi
SystemRequirements	GNU make, C++11
Enhances
URL	https://pqsfinder.fi.muni.cz
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	pqsfinder_2.14.1.tar.gz
Windows Binary	pqsfinder_2.14.1.zip
macOS Binary (x86_64)	pqsfinder_2.14.1.tgz
macOS Binary (arm64)	pqsfinder_2.14.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/pqsfinder
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/pqsfinder
Bioc Package Browser	https://code.bioconductor.org/browse/pqsfinder/
Package Short Url	https://bioconductor.org/packages/pqsfinder/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive