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>
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 | 1.10.1 |
| 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, stringr |
| Linking To | Rcpp, BH (>= 1.66.0) |
| 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_1.10.1.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/pqsfinder/ |
| Package Short Url | https://bioconductor.org/packages/pqsfinder/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.8 | Source Archive |