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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("triplex")
In most cases, you don't need to download the package archive at all.
triplex
|
This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see triplex.
Search and visualize intramolecular triplex-forming sequences in DNA
Bioconductor version: 3.1
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>
Citation (from within R,
enter citation("triplex")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("triplex")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("triplex")
| R Script | Triplex User Guide | |
| Reference Manual | ||
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | GeneRegulation, SequenceMatching, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (3 years) |
| License | BSD_2_clause + file LICENSE |
| Depends | R (>= 2.15.0), S4Vectors(>= 0.5.14), IRanges(>= 1.99.1), XVector(>= 0.7.3), Biostrings(>= 2.33.3) |
| Imports | methods, grid, GenomicRanges |
| LinkingTo | S4Vectors, IRanges, XVector, Biostrings |
| Suggests | rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer, GenomeGraphs |
| SystemRequirements | |
| Enhances | |
| URL | http://www.fi.muni.cz/~lexa/triplex/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | triplex_1.8.0.tar.gz |
| Windows Binary | triplex_1.8.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | triplex_1.8.0.tgz |
| Mac OS X 10.9 (Mavericks) | triplex_1.8.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/triplex/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/triplex/ |
| Package Downloads Report | Download Stats |
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