Package: katdetectr
Title: Detection, Characterization and Visualization of Kataegis in
        Sequencing Data
Version: 1.2.0
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 = c("aut"),
           comment = c(ORCID = "0000-0001-7767-7923")),
    person("Harmen", "van de Werken", , "h.vandewerken@erasmusmc.nl", role = c("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: BiocParallel (>= 1.26.2), changepoint (>= 2.2.3),
        changepoint.np (>= 1.0.3), checkmate (>= 2.0.0), dplyr (>=
        1.0.8), GenomicRanges (>= 1.44.0), GenomeInfoDb (>= 1.28.4),
        IRanges (>= 2.26.0), maftools (>= 2.10.5), methods (>= 4.1.3),
        rlang (>= 1.0.2), S4Vectors (>= 0.30.2), tibble (>= 3.1.6),
        VariantAnnotation (>= 1.38.0), Biobase (>= 2.54.0), Rdpack (>=
        2.3.1), ggplot2 (>= 3.3.5), tidyr (>= 1.2.0), BSgenome (>=
        1.62.0), ggtext (>= 0.1.1), BSgenome.Hsapiens.UCSC.hg19 (>=
        1.4.3), BSgenome.Hsapiens.UCSC.hg38 (>= 1.4.4), plyranges (>=
        1.17.0)
Suggests: scales (>= 1.2.0), knitr (>= 1.37), rmarkdown (>= 2.13),
        testthat (>= 3.0.0), BiocStyle (>= 2.26.0)
RdMacros: Rdpack
VignetteBuilder: knitr
biocViews: WholeGenome, Software, SNP, Sequencing, Classification,
        VariantAnnotation
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/katdetectr
git_branch: RELEASE_3_17
git_last_commit: c4808c6
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-25
NeedsCompilation: no
Packaged: 2023-04-25 21:31:40 UTC; biocbuild
Author: Daan Hazelaar [aut, cre] (<https://orcid.org/0000-0002-7513-6813>),
  Job van Riet [aut] (<https://orcid.org/0000-0001-7767-7923>),
  Harmen van de Werken [ths] (<https://orcid.org/0000-0002-9794-1477>)
Maintainer: Daan Hazelaar <daanhazelaar@gmail.com>
Built: R 4.3.1; ; 2023-07-15 20:50:39 UTC; unix
