Package: SingleMoleculeGenomicsIO
Title: Tools for reading single molecule genomics data
Version: 0.1.9
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)
SystemRequirements: GNU make
Config/roxygen2/version: 8.1.1
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://fmicompbio.r-universe.dev
Date/Publication: 2026-10-19 07:51:20 UTC
RemoteUrl: https://github.com/fmicompbio/SingleMoleculeGenomicsIO
RemoteRef: HEAD
RemoteSha: 8c2db76b5182cc8223fff51c362662f1778f5cb5
NeedsCompilation: yes
Packaged: 2026-10-26 10:48:01 UTC; root
Author: Michael Stadler [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-2269-4934>),
  Charlotte Soneson [aut] (ORCID:
    <https://orcid.org/0000-0003-3833-2169>),
  Panagiotis Papasaikas [aut] (ORCID:
    <https://orcid.org/0000-0002-1640-7636>),
  Sebastien Smallwood [aut] (ORCID:
    <https://orcid.org/0009-0006-8466-2459>),
  Friedrich Miescher Institute for Biomedical Research [cph]
Maintainer: Michael Stadler <michael.stadler@fmi.ch>