SingleMoleculeGenomicsIO/DESCRIPTION at devel · fmicompbio/SingleMoleculeGenomicsIO · GitHub

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Package: SingleMoleculeGenomicsIO
Title: Tools for reading single molecule genomics data
Version: 0.1.3
Authors@R: c(
    person("Michael", "Stadler", , "michael.stadler@fmi.ch",
           role = c("aut", "cre"), comment = c(ORCID = "0000-0002-2269-4934")),
    person("Charlotte", "Soneson", , "charlotte.soneson@fmi.ch",
           role = "aut", comment = c(ORCID = "0000-0003-3833-2169")),
    person("Panagiotis", "Papasaikas", , "panagiotis.papasaikas@fmi.ch",
           role = "aut", comment = c(ORCID = "0000-0002-1640-7636")),
    person("Sebastien", "Smallwood", , "sebastien.smallwood@fmi.ch",
           role = "aut", comment = c(ORCID = "0009-0006-8466-2459")),
    person("Friedrich Miescher Institute for Biomedical Research", role = "cph")
  )
Description: Provides tools for reading of single-molecule genomics data
    from different file formats in R. The package includes functions for reading
    collapsed or read-level data from modBAM, bedMethyl and `modkit extract`
    tabular files, as well as C-to-T conversion based BAM files, as
    `SummarizedExperiment` objects.
License: MIT + file LICENSE
URL: https://github.com/fmicompbio/SingleMoleculeGenomicsIO,
    https://fmicompbio.github.io/SingleMoleculeGenomicsIO
BugReports: https://github.com/fmicompbio/SingleMoleculeGenomicsIO/issues
Depends:
    R (>= 4.1.0)
Imports:
    BiocGenerics,
    BiocParallel,
    Biostrings,
    BSgenome,
    cli,
    data.table,
    dplyr,
    GenomicRanges,
    ggplot2,
    IRanges,
    methods,
    Rcpp,
    rlang,
    S4Vectors,
    Seqinfo,
    SparseArray,
    SummarizedExperiment,
    tibble,
    tidyr,
    utils
Suggests:
    BiocIO,
    BiocManager,
    knitr,
    MatrixGenerics,
    R.utils,
    rmarkdown,
    Rsamtools,
    sessioninfo,
    SimpleUpset,
    testthat (>= 3.0.0),
    withr
LinkingTo:
    cli,
    Rcpp,
    Rhtslib
VignetteBuilder:
    knitr
biocViews: Epigenetics, LongRead
Config/testthat/edition: 3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
SystemRequirements: GNU make