pqsfinder

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see pqsfinder.

Identification of potential quadruplex forming sequences


Bioconductor version: 3.7

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 "3.5") 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")
pqsfinder: User Guide HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GeneRegulation, MotifDiscovery, SequenceMatching, Software
Version 1.8.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License BSD_2_clause + file LICENSE
Depends Biostrings
Imports Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods
System Requirements GNU make, C++11
URL
See More
Suggests BiocStyle, knitr, Gviz, rtracklayer, ggplot2, BSgenome.Hsapiens.UCSC.hg38, testthat
Linking To Rcpp, BH (>= 1.62.0)
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 pqsfinder_1.8.0.tar.gz
Windows Binary pqsfinder_1.8.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) pqsfinder_1.8.0.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 https://bioconductor.org/packages/pqsfinder/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive