triplex
This is the development version of triplex; for the stable release version, see triplex.
Search and visualize intramolecular triplex-forming sequences in DNA
Bioconductor version: Development (3.24)
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("triplex")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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")| Triplex User Guide | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneRegulation, SequenceMatching, Software |
| Version | 1.53.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (13.5 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 |
| System Requirements | |
| URL | http://www.fi.muni.cz/~lexa/triplex/ |
See More
| Suggests | rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer |
| Linking To | S4Vectors, IRanges, XVector, Biostrings |
| 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 | triplex_1.53.0.tar.gz |
| Windows Binary (x86_64) | triplex_1.53.0.zip |
| macOS Binary (big-sur-x86_64) | triplex_1.53.0.tgz |
| macOS Binary (sonoma-arm64) | triplex_1.53.0.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 |