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Structstrings

This is the development version of Structstrings; for the stable release version, see Structstrings.

Implementation of the dot bracket annotations with Biostrings


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("Structstrings")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Structstrings HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, DataImport, DataRepresentation, Infrastructure, SequenceMatching, Sequencing, Software
Version 1.19.0
In Bioconductor since BioC 3.9 (R-3.6) (5 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
System Requirements
URL https://github.com/FelixErnst/Structstrings
Bug Reports https://github.com/FelixErnst/Structstrings/issues
See More
Suggests testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle
Linking To IRanges, S4Vectors
Enhances
Depends On Me tRNA, tRNAdbImport
Imports Me tRNAscanImport
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package Structstrings_1.19.0.tar.gz
Windows Binary Structstrings_1.19.0.zip
macOS Binary (x86_64) Structstrings_1.19.0.tgz
macOS Binary (arm64) Structstrings_1.19.0.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