Package: katdetectr
Title: Detection, Characterization and Visualization of Kataegis in Sequencing Data
Version: 1.13.0
Date: 2023-02-14
Authors@R: c(
    person("Daan", "Hazelaar", , "daanhazelaar@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-7513-6813")),
    person("Job", "van Riet", , "j.vanriet@erasmusmc.nl", role = "aut",
           comment = c(ORCID = "0000-0001-7767-7923")),
    person("Harmen", "van de Werken", , "h.vandewerken@erasmusmc.nl", role = "ths",
           comment = c(ORCID = "0000-0002-9794-1477"))
  )
Description: Kataegis refers to the occurrence of regional hypermutation
    and is a phenomenon observed in a wide range of malignancies. Using
    changepoint detection katdetectr aims to identify putative kataegis
    foci from common data-formats housing genomic variants.  Katdetectr
    has shown to be a robust package for the detection, characterization
    and visualization of kataegis.
License: GPL-3 + file LICENSE
URL: https://doi.org/doi:10.18129/B9.bioc.katdetectr
BugReports: https://github.com/ErasmusMC-CCBC/katdetectr/issues
Depends:
    R (>= 4.2)
Imports: 
    Biobase (>= 2.54.0),
    BiocParallel (>= 1.26.2),
    BSgenome (>= 1.62.0),
    BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.3),
    BSgenome.Hsapiens.UCSC.hg38 (>= 1.4.4),
    changepoint (>= 2.2.3),
    changepoint.np (>= 1.0.3),
    checkmate (>= 2.0.0),
    dplyr (>= 1.0.8),
    GenomeInfoDb (>= 1.28.4),
    GenomicRanges (>= 1.44.0),
    ggplot2 (>= 3.3.5),
    ggtext (>= 0.1.1),
    IRanges (>= 2.26.0),
    maftools (>= 2.10.5),
    methods (>= 4.1.3),
    plyranges (>= 1.17.0),
    Rdpack (>= 2.3.1),
    rlang (>= 1.0.2),
    S4Vectors (>= 0.30.2),
    scales (>= 1.2.0),
    tibble (>= 3.1.6),
    tidyr (>= 1.2.0),
    tools,
    utils,
    VariantAnnotation (>= 1.38.0)
Suggests: 
    BiocStyle (>= 2.26.0),
    knitr (>= 1.37),
    rmarkdown (>= 2.13),
    stats,
    testthat (>= 3.0.0)
VignetteBuilder: 
    knitr
RdMacros: 
    Rdpack
biocViews: WholeGenome, Software, SNP, Sequencing, Classification,
    VariantAnnotation
Config/testthat/edition: 3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
git_url: https://git.bioconductor.org/packages/katdetectr
git_branch: devel
git_last_commit: 01624d8
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
