pqsfinder

DOI: 10.18129/B9.bioc.pqsfinder    

This is the development version of pqsfinder; to use it, please install the devel version of Bioconductor.

Identification of potential quadruplex forming sequences

Bioconductor version: Development (3.10)

Pqsfinder detects DNA 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>

Citation (from within R, enter citation("pqsfinder")):

Installation

To install this package, start R (version "3.6") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 2.1.1
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 (>= 1.69.0)
Suggests BiocStyle, knitr, Gviz, rtracklayer, ggplot2, BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi
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_2.1.1.tar.gz
Windows Binary pqsfinder_2.1.1.zip
Mac OS X 10.11 (El Capitan) pqsfinder_2.1.1.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

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