Package: Modstrings
Type: Package
Title: Implementation of Biostrings to work with nucleotide sequences
        containing modified nucleotides
Version: 1.0.3
Date: 2019-06-25
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, assertive, BiocGenerics, GenomicRanges, S4Vectors,
        IRanges, XVector, stringi, stringr
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'
VignetteBuilder: knitr
RoxygenNote: 6.1.1
BugReports: https://github.com/FelixErnst/Modstrings/issues
git_url: https://git.bioconductor.org/packages/Modstrings
git_branch: RELEASE_3_9
git_last_commit: 0322f64
git_last_commit_date: 2019-06-25
Date/Publication: 2019-06-25
NeedsCompilation: no
Packaged: 2019-06-26 05:20:30 UTC; biocbuild
Author: Felix G.M. Ernst [aut, cre] (<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 3.6.0; ; 2019-06-26 13:28:39 UTC; windows
