Package: Structstrings
Title: Implementation of the dot bracket annotations with Biostrings
Version: 1.28.0
Date: 2025-09-22
Authors@R: person("Felix G.M.","Ernst",
                  email = "felix.gm.ernst@outlook.com",
                  role = c("aut", "cre"),
                  comment = c(ORCID = "0000-0001-5064-0928"))
Description: 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.
License: Artistic-2.0
Encoding: UTF-8
LazyData: false
biocViews: DataImport, DataRepresentation, Infrastructure, Sequencing,
        Software, Alignment, SequenceMatching
Depends: R (>= 4.0), S4Vectors (>= 0.47.2), IRanges (>= 2.23.9),
        Biostrings (>= 2.57.2)
LinkingTo: IRanges, S4Vectors
Imports: methods, BiocGenerics, XVector, stringr, stringi, crayon,
        grDevices
Suggests: testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle
VignetteBuilder: knitr
RoxygenNote: 7.3.3
Collate: 'Structstrings.R' 'AllGenerics.R'
        'Structstrings-DotBracket-io.R'
        'Structstrings-DotBracketDataFrame.R'
        'Structstrings-DotBracketString.R'
        'Structstrings-DotBracketStringSet.R'
        'Structstrings-DotBracketStringSetList.R'
        'Structstrings-LoopIndexList.R'
        'Structstrings-StructuredXStringSet.R'
        'Structstrings-alphabet.R' 'Structstrings-conversion.R'
        'utils.R' 'zzz.R'
NeedsCompilation: yes
BugReports: https://github.com/FelixErnst/Structstrings/issues
URL: https://github.com/FelixErnst/Structstrings
Config/pak/sysreqs: libicu-dev zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28 12:49:46 UTC
RemoteUrl: https://github.com/bioc/Structstrings
RemoteRef: RELEASE_3_23
RemoteSha: 38d447a0669aca6ce85f44eb4890234933f1a2f2
Packaged: 2026-11-01 17:32:16 UTC; root
Author: Felix G.M. Ernst [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-5064-0928>)
Maintainer: Felix G.M. Ernst <felix.gm.ernst@outlook.com>