pqsfinder

DOI: 10.18129/B9.bioc.pqsfinder    

This is the development version of pqsfinder; for the stable release version, see pqsfinder.

Identification of potential quadruplex forming sequences

Bioconductor version: Development (3.9)

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>

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")
BiocManager::install("pqsfinder", version = "3.9")

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 1.11.0
In Bioconductor since BioC 3.3 (R-3.3) (2.5 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_1.11.0.tar.gz
Windows Binary pqsfinder_1.11.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) pqsfinder_1.11.0.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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