triplex

DOI: 10.18129/B9.bioc.triplex  

Search and visualize intramolecular triplex-forming sequences in DNA

Bioconductor version: Release (3.16)

This package provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many cannonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.

Author: Jiri Hon, Matej Lexa, Tomas Martinek and Kamil Rajdl with contributions from Daniel Kopecek

Maintainer: Jiri Hon <jiri.hon at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("triplex")

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("triplex")

 

PDF	R Script	Triplex User Guide
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GeneRegulation, SequenceMatching, Software
Version	1.38.0
In Bioconductor since	BioC 2.12 (R-3.0) (10 years)
License	BSD_2_clause + file LICENSE
Depends	R (>= 2.15.0), S4Vectors(>= 0.5.14), IRanges(>= 2.5.27), XVector(>= 0.11.6), Biostrings(>= 2.39.10)
Imports	methods, grid, GenomicRanges
LinkingTo	S4Vectors, IRanges, XVector, Biostrings
Suggests	rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer
SystemRequirements
Enhances
URL	http://www.fi.muni.cz/~lexa/triplex/
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	triplex_1.38.0.tar.gz
Windows Binary	triplex_1.38.0.zip
macOS Binary (x86_64)	triplex_1.38.0.tgz
macOS Binary (arm64)	triplex_1.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/triplex
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/triplex
Bioc Package Browser	https://code.bioconductor.org/browse/triplex/
Package Short Url	https://bioconductor.org/packages/triplex/
Package Downloads Report	Download Stats