DESCRIPTION

Package: Structstrings
Title: Implementation of the dot bracket annotations with Biostrings
Version: 1.23.1
Date: 2024-11-02
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 (>= 0.27.12),
    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: 7.3.2
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