Package: Modstrings
Type: Package
Title: Working with modified nucleotide sequences
Version: 1.29.0
Date: 2022-12-24
Authors@R: c(person("Felix G.M.", 
                    "Ernst", 
                    email = "felix.gm.ernst@outlook.com", 
                    role = c("aut", "cre"),
                    comment = c(ORCID = "0000-0001-5064-0928")),
             person("Denis L.J.", 
                    "Lafontaine", 
                    email = "denis.lafontaine@ulb.ac.be", 
                    role = c("ctb", "fnd")))
Description: Representing nucleotide modifications in a nucleotide
        sequence is usually done via special characters from a number
        of sources. This represents a challenge to work with in R and
        the Biostrings package. The Modstrings package implements this
        functionallity for RNA and DNA sequences containing modified
        nucleotides by translating the character internally in order to
        work with the infrastructure of the Biostrings package. For
        this the ModRNAString and ModDNAString classes and derivates
        and functions to construct and modify these objects despite the
        encoding issues are implemenented. In addition the conversion
        from sequences to list like location information (and the
        reverse operation) is implemented as well.
License: Artistic-2.0
Encoding: UTF-8
biocViews: DataImport, DataRepresentation, Infrastructure, Sequencing,
        Software
Depends: R (>= 3.6), Biostrings (>= 2.79.3)
Imports: methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges,
        XVector, stringi, stringr, crayon, grDevices
Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis
Collate: 'Modstrings.R' 'AllGenerics.R'
        'Modstrings-external-functions.R'
        'Modstrings-external-C-calls.R' 'Modstrings-ModStringCodec.R'
        'Modstrings-ModString.R' 'Modstrings-ModStringSet.R'
        'Modstrings-ModStringViews.R' 'Modstrings-MaskedModString.R'
        'Modstrings-ModStringCodec-data.R'
        'Modstrings-ModStringSet-io.R' 'Modstrings-ModStringSetList.R'
        'Modstrings-QualityScaledModStringSet.R'
        'Modstrings-letterFrequency.R' 'Modstrings-modifyNucleotide.R'
        'Modstrings-replaceLetterAt.R' 'Modstrings-sanitize.R'
        'Modstrings-separate.R' 'Modstrings-seqtype.R' 'datasets.R'
        'utils.R' 'zzz.R'
VignetteBuilder: knitr
RoxygenNote: 7.3.3
BugReports: https://github.com/FelixErnst/Modstrings/issues
Config/pak/sysreqs: libicu-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:49:42 UTC
RemoteUrl: https://github.com/bioc/Modstrings
RemoteRef: HEAD
RemoteSha: 4509228b0af0b505d0a14a5f87fa28996a89f553
NeedsCompilation: no
Packaged: 2026-07-04 07:02:55 UTC; root
Author: Felix G.M. Ernst [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-5064-0928>),
  Denis L.J. Lafontaine [ctb, fnd]
Maintainer: Felix G.M. Ernst <felix.gm.ernst@outlook.com>