Package: MutSeqRData
Title: Experimental Data for MutSeqR Examples
Version: 0.99.4
Authors@R: c(
    person("Annette E.", "Dodge",
      email = "annette.dodge@hc-sc.gc.ca",
      role = "aut",
      comment = c(ORCID = "0000-0002-0446-9055")
    ),
    person("Andrew", "Williams",
      role = "aut",
      comment = c(ORCID = "0000-0002-7637-7686")
    ),
    person("Danielle P.M.", "LeBlanc",
      role = "aut",
      comment = c(ORCID = "0000-0002-3847-8371")
    ),
    person("David M.", "Schuster",
      role = "aut",
      comment = c(ORCID = "0009-0001-6316-4358")
    ),
    person("Elena", "Esina", 
      role = "aut",
      comment = c(ORCID = "0009-0002-3443-378X")
    ),
    person("Clint C.", "Valentine", role = "aut"),
    person("Jesse J.", "Salk", role = "aut"),
    person("Alexander Y.", "Maslov", role = "aut"),
    person("Christopher", "Bradley", role = "aut"),
    person("Carole L.", "Yauk",
      role = "aut",
      comment = c(ORCID = "0000-0002-6725-3454")
    ),
    person("Francesco", "Marchetti",
      role = "aut",
      comment = c(ORCID = "0000-0002-9435-4867")
    ),    
    person("Matthew J.", "Meier",
      email = "matthew.meier@hc-sc.gc.ca",
      role = c("aut", "cre"),
      comment = c(ORCID = "0000-0001-8199-8754")
    ),
    person("Geronimo", "Matteo",
      role = "ctb",
      comment = c(ORCID = "0000-0003-0819-4471")
    )
  )
Description: Experimental data for use with the MutSeqR vignette and examples. This dataset is taken from LeBlanc et al., 2022. 24 MutaMouse animals were exposed to one of three doses of benzo[a]pyrene or a vehicle control for 28 days by oral gavage. 28 days after the end of the exposure, bone marrow of the femurs was harvested from euthanized animals. DNA extraction was conducted via DNeasy Blood and Tissue kit. DNA samples were sequenced using TwinStrand's Duplex Sequencing on the Mouse Mutagenesis Panel at > 10,000 depth. The Mouse Mutagenesis Panel comprises 20 2.4kb genomic targets with one located on each mouse autosome (two on chromosome 1). Pre-processing of sequence reads was redone since publication using an updated version of TwinStrand's Mutagenesis App (v. 3.20.1) which produced tabular mutation data files for each sample. Data contained herein are only those required for running MutSeqR examples and vignette.
License: MIT + file LICENSE
Depends: R (>= 3.5.0)
Encoding: UTF-8
biocViews: ExperimentHub, Mus_musculus_Data, Genome, Somatic,
        SequencingData
Suggests: BiocStyle, knitr, rmarkdown
RoxygenNote: 7.3.1
VignetteBuilder: knitr
BugReports: https://github.com/EHSRB-BSRSE-Bioinformatics/MutSeqRData/issues
URL: https://github.com/EHSRB-BSRSE-Bioinformatics/MutSeqRData/
git_url: https://git.bioconductor.org/packages/MutSeqRData
git_branch: devel
git_last_commit: 121dd0f
git_last_commit_date: 2025-12-09
Repository: Bioconductor 3.23
Date/Publication: 2026-01-13
NeedsCompilation: no
Packaged: 2026-01-13 16:34:36 UTC; biocbuild
Author: Annette E. Dodge [aut] (ORCID: <https://orcid.org/0000-0002-0446-9055>),
  Andrew Williams [aut] (ORCID: <https://orcid.org/0000-0002-7637-7686>),
  Danielle P.M. LeBlanc [aut] (ORCID:
    <https://orcid.org/0000-0002-3847-8371>),
  David M. Schuster [aut] (ORCID:
    <https://orcid.org/0009-0001-6316-4358>),
  Elena Esina [aut] (ORCID: <https://orcid.org/0009-0002-3443-378X>),
  Clint C. Valentine [aut],
  Jesse J. Salk [aut],
  Alexander Y. Maslov [aut],
  Christopher Bradley [aut],
  Carole L. Yauk [aut] (ORCID: <https://orcid.org/0000-0002-6725-3454>),
  Francesco Marchetti [aut] (ORCID:
    <https://orcid.org/0000-0002-9435-4867>),
  Matthew J. Meier [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8199-8754>),
  Geronimo Matteo [ctb] (ORCID: <https://orcid.org/0000-0003-0819-4471>)
Maintainer: Matthew J. Meier <matthew.meier@hc-sc.gc.ca>
