Package: Modstrings
Type: Package
Title: Working with modified nucleotide sequences
Version: 1.25.0
Date: 2022-08-13
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 (>= 2.51.5)
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: 7.2.1
BugReports: https://github.com/FelixErnst/Modstrings/issues
git_url: https://git.bioconductor.org/packages/Modstrings
git_branch: devel
git_last_commit: ea5c7b3
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-05 00:27:17 UTC; biocbuild
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>
Built: R 4.5.0; ; 2025-06-05 13:26:47 UTC; windows
