Package: XNAString
Title: Efficient Manipulation of Modified Oligonucleotide Sequences
Version: 1.16.0
Authors@R: c(person(given = "Anna",
                  family = "Górska",
                  role = "aut"),
            person(given = "Marianna",
                   family = "Plucinska",
                   role = c("aut", "cre"),
                   email = "marianna.plucinska@roche.com"),
            person(given = "Lykke",
                   family = "Pedersen",
                   role = "aut"),
            person(given = "Lukasz",
                   family = "Kielpinski",
                   role = "aut"),
            person(given = "Disa",
                   family = "Tehler",
                   role = "aut"),
            person(given = "Peter H.",
                   family = "Hagedorn",
                   role = "aut",
                   email = "peter.hagedorn@roche.com"))
Date: 31.05.2021
Description: The XNAString package allows for description of base sequences and 
    associated chemical modifications in a single object. XNAString is able to 
    capture single stranded, as well as double stranded molecules. Chemical 
    modifications are represented as independent strings associated with different 
    features of the molecules (base sequence, sugar sequence, backbone sequence,
    modifications) and can be read or written to a HELM notation. It also enables
    secondary structure prediction using RNAfold from ViennaRNA. XNAString is 
    designed to be efficient representation of nucleic-acid based therapeutics, 
    therefore it stores information about target sequences and provides interface
    for matching and alignment functions from Biostrings and pwalign packages.
biocViews: SequenceMatching, Alignment, Sequencing, Genetics
Depends: R (>= 4.1)
Imports: utils, Biostrings, pwalign, BSgenome, data.table,
        GenomicRanges, IRanges, methods, Rcpp, stringi, S4Vectors,
        future.apply, stringr, formattable, stats
Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat,
        BSgenome.Hsapiens.UCSC.hg38, pander
LinkingTo: Rcpp
License: GPL-2
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
Collate: 'RcppExports.R' 'utils.R' 'xnaStringSetClass.R'
        'setterGetter.R' 'classUnion.R' 'xnaStringClass.R'
        'XNAString2Helm.R' 'XNAStringFromHelm.R' 'alphabetFrequency.R'
        'data.R' 'dictFromMimir.R' 'dinucleotideFrequency.R'
        'globals.R' 'helm2String.R' 'matchPDict.R' 'matchPattern.R'
        'pairwiseAlignment.R' 'predictDuplexStructure.R'
        'predictMfeStructure.R' 'reverseComplement.R'
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/XNAString
git_branch: RELEASE_3_21
git_last_commit: d1ff0c2
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: yes
Packaged: 2025-04-15 23:14:17 UTC; biocbuild
Author: Anna Górska [aut],
  Marianna Plucinska [aut, cre],
  Lykke Pedersen [aut],
  Lukasz Kielpinski [aut],
  Disa Tehler [aut],
  Peter H. Hagedorn [aut]
Maintainer: Marianna Plucinska <marianna.plucinska@roche.com>
Built: R 4.5.0; aarch64-apple-darwin20; 2025-04-16 04:11:09 UTC; unix
