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("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 | ||
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 |