Package: MutSeqR
Title: Analysis of Error-Corrected Sequencing Data for Mutation
        Detection
Version: 1.1.0
Date: 2025-12-09
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",
      comment = c(ORCID = "0000-0001-5630-7368")),
    person("Jesse J.", "Salk", role = "aut",
      comment = c(ORCID = "0000-0002-7804-0550")),
    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")),
    person("Health Canada's Genomics Research and Development Initiative", role = "fnd"),
    person("Canada Research Chairs Program", role = "fnd", comment = "CRC-2020-00060"),
    person("Burroughs Wellcome Fund", role = "fnd")
  )
Description: Standard methods for analysis of mutation data following
        error- corrected sequencing (ECS) for the purpose of
        mutagencity assessment. Functions include importing the
        mutation lists provided by a variant caller, and a set of
        analytical tools for statistical testing and visualization of
        mutation data; comparison to COSMIC and/or germline signatures;
        etc.
License: MIT + file LICENSE
Depends: R (>= 4.5.0)
biocViews: Sequencing, SomaticMutation, Visualization,
        GenomicVariation, DriverMutation, StatisticalMethod, GeneTarget
Imports: BiocGenerics, Biostrings, BSgenome, data.table, dplyr,
        GenomicRanges, ggplot2, here, IRanges, ggdendro, magrittr,
        methods, plyranges, rlang, S4Vectors, Seqinfo, stats, stringr,
        SummarizedExperiment, tibble, tidyr, utils, VariantAnnotation
Suggests: binom, BiocManager, BiocStyle, bs4Dash,
        BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, car,
        colorspace, dendsort, doBy, DT, ExperimentHub, fmsb, fs,
        ggrepel, gtools, htmltools, httr, knitr, lme4, magick,
        MutSeqRData, openxlsx, packcircles, patchwork, RColorBrewer,
        reticulate, rmarkdown, scales, shiny, testthat (>= 3.0.0),
        trackViewer, withr, yaml, xml2
VignetteBuilder: knitr
Config/reticulate: list( packages = list( list(package =
        "SigProfilerAssignment"), list(package =
        "SigProfilerExtractor"), list(package =
        "SigProfilerMatrixGenerator") ) )
Config/testthat/edition: 3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
BugReports: https://github.com/EHSRB-BSRSE-Bioinformatics/MutSeqR/issues
URL: https://ehsrb-bsrse-bioinformatics.github.io/MutSeqR/
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:06:12 UTC
RemoteUrl: https://github.com/bioc/MutSeqR
RemoteRef: HEAD
RemoteSha: 99d54af33c2e9ac45b8928eecca49f089630ad3c
NeedsCompilation: no
Packaged: 2026-07-03 13:15:08 UTC; root
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] (ORCID:
    <https://orcid.org/0000-0001-5630-7368>),
  Jesse J. Salk [aut] (ORCID: <https://orcid.org/0000-0002-7804-0550>),
  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>),
  Health Canada's Genomics Research and Development Initiative [fnd],
  Canada Research Chairs Program [fnd] (CRC-2020-00060),
  Burroughs Wellcome Fund [fnd]
Maintainer: Matthew J. Meier <matthew.meier@hc-sc.gc.ca>