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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("triplex")
In most cases, you don't need to download the package archive at all.
triplex
Search and visualize intramolecular triplex-forming sequences in DNA
Bioconductor version: 3.0
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:
source("http://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 | 1.6.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) |
| License | BSD_2_clause + file LICENSE |
| Depends | R (>= 2.15.0), S4Vectors, IRanges(>= 1.99.1), XVector(>= 0.5.3), 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_1.6.0.tar.gz |
| Windows Binary | triplex_1.6.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | triplex_1.6.0.tgz |
| Mac OS X 10.9 (Mavericks) | triplex_1.6.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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