Structstrings

DOI: 10.18129/B9.bioc.Structstrings  

Implementation of the dot bracket annotations with Biostrings

Bioconductor version: Release (3.16)

The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.

Author: Felix G.M. Ernst [aut, cre]

Maintainer: Felix G.M. Ernst <felix.gm.ernst at outlook.com>

Installation

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

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

BiocManager::install("Structstrings")

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("Structstrings")

 

HTML	R Script	Structstrings
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, DataImport, DataRepresentation, Infrastructure, SequenceMatching, Sequencing, Software
Version	1.14.0
In Bioconductor since	BioC 3.9 (R-3.6) (4 years)
License	Artistic-2.0
Depends	R (>= 4.0), S4Vectors(>= 0.27.12), IRanges(>= 2.23.9), Biostrings(>= 2.57.2)
Imports	methods, BiocGenerics, XVector, stringr, stringi, crayon, grDevices
LinkingTo	IRanges, S4Vectors
Suggests	testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/FelixErnst/Structstrings
BugReports	https://github.com/FelixErnst/Structstrings/issues
Depends On Me	tRNA, tRNAdbImport
Imports Me	tRNAscanImport
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	Structstrings_1.14.0.tar.gz
Windows Binary	Structstrings_1.14.0.zip
macOS Binary (x86_64)	Structstrings_1.14.0.tgz
macOS Binary (arm64)	Structstrings_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Structstrings
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Structstrings
Bioc Package Browser	https://code.bioconductor.org/browse/Structstrings/
Package Short Url	https://bioconductor.org/packages/Structstrings/
Package Downloads Report	Download Stats