pqsfinder

DOI: 10.18129/B9.bioc.pqsfinder    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see pqsfinder.

Identification of potential quadruplex forming sequences

Bioconductor version: 3.8

The main functionality of this package is to detect DNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, this package is able to detect sequences responsible for G4s folded from imperfect G-runs containing bulges or mismatches and as such is more sensitive than competing algorithms.

Author: Jiri Hon, Matej Lexa and Tomas Martinek

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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	1.10.1
In Bioconductor since	BioC 3.3 (R-3.3) (3 years)
License	BSD_2_clause + file LICENSE
Depends	Biostrings
Imports	Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods
LinkingTo	Rcpp, BH (>= 1.66.0)
Suggests	BiocStyle, knitr, Gviz, rtracklayer, ggplot2, BSgenome.Hsapiens.UCSC.hg38, testthat, stringr
SystemRequirements	GNU make, C++11
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	pqsfinder_1.10.1.tar.gz
Windows Binary	pqsfinder_1.10.1.zip
Mac OS X 10.11 (El Capitan)	pqsfinder_1.10.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/pqsfinder
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/pqsfinder
Package Short Url	http://bioconductor.org/packages/pqsfinder/
Package Downloads Report	Download Stats