DOI: 10.18129/B9.bioc.Structstrings    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see Structstrings.

Implementation of the dot bracket annotations with Biostrings

Bioconductor version: 3.13

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 < at>

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biocViews Alignment, DataImport, DataRepresentation, Infrastructure, SequenceMatching, Sequencing, Software
Version 1.8.0
In Bioconductor since BioC 3.9 (R-3.6) (2.5 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
LinkingTo IRanges, S4Vectors
Suggests testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle
Depends On Me tRNA, tRNAdbImport
Imports Me tRNAscanImport
Suggests Me
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