Package: OikScrambling
Type: Package
Title: Oikopleura Genome Comparison Study
Version: 5.1.0
Date: 2023-11-02
Authors@R: c(
    person(given = "Aleksandra",
           family = "Bliznina",
           role = c("aut"),
           email = "Aleksandra.Bliznina2@oist.jp",
           comment = c(ORCID = "0000-0001-5031-8023")),
    person(given = "Michael",
           family = "Mansfield",
           role = c("aut"),
           email = "michael.mansfield@oist.jp",
           comment = c(ORCID = "0000-0003-4717-4721")),
    person(given = "Charles",
           family = "Plessy",
           role = c("aut", "cre"),
           email = "charles.plessy@oist.jp",
           comment = c(ORCID = "0000-0001-7410-6295")))
Description: Analysis of the Oikopleura breakpoint dataset for the scrambling
    project.  The data is distributed in a drat repository on GitHub at
    <https://oist.github.io/plessy_oikgenomes_drat/>.
URL: https://github.com/oist/LuscombeU_OikScrambling
License: BSD_3_clause + file LICENSE
Encoding: UTF-8
LazyData: true
Depends:
  R (>= 4.1.0),
  BSgenome,
  GenomicBreaks (>= 0.14.3),
  GenomicRanges,
  ggplot2
Imports:
  CNEr,
  ggmsa,
  pheatmap,
  msa,
  rtracklayer,
  S4Vectors,
  TFBSTools,
  heatmaps,
  GenomicFeatures,
  IRanges,
  GenomeInfoDb,
  stats,
  graphics,
  Biostrings,
RoxygenNote: 7.2.3
Roxygen: list(markdown = TRUE)
Suggests:
  BreakpointsData (>= 3.11.0),
  BSgenome.Oidioi.OIST.OKI2018.I69,
  BSgenome.Oidioi.OIST.OSKA2016v1.9,
  BSgenome.Oidioi.genoscope.OdB3,
  BSgenome.Oidioi.OIST.Bar2.p4,
  BSgenome.Oidioi.OIST.KUM.M3.7f,
  BSgenome.Oidioi.OIST.AOM.5.5f,
  genoPlotR,
  ggplot2,
  gridExtra,
  Gviz,
  knitr,
  plyranges,
  rmarkdown,
  UpSetR
VignetteBuilder: knitr
Additional_repositories: https://oist.github.io/plessy_oikgenomes_drat/
