Package: katdetectr
Title: Detection, Characterization and Visualization of Kataegis in
        Sequencing Data
Version: 1.12.0
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
Config/pak/sysreqs: make libbz2-dev libicu-dev libjpeg-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:17:25 UTC
RemoteUrl: https://github.com/bioc/katdetectr
RemoteRef: RELEASE_3_22
RemoteSha: 3e318d946a21e4970bddc91f20184dbf0f81925c
NeedsCompilation: no
Packaged: 2025-11-11 15:36:32 UTC; root
Author: Daan Hazelaar [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-7513-6813>),
  Job van Riet [aut] (ORCID: <https://orcid.org/0000-0001-7767-7923>),
  Harmen van de Werken [ths] (ORCID:
    <https://orcid.org/0000-0002-9794-1477>)
Maintainer: Daan Hazelaar <daanhazelaar@gmail.com>
Built: R 4.5.2; ; 2025-11-11 15:45:16 UTC; windows
