Package: LACHESIS
Title: Functions used to analyze early tumor evolution from whole
        genome sequencing data
Version: 0.99.5
Authors@R: c(
  person(given = "Verena",
         family = "Körber",
         role = c("aut", "cre"),
         email = "verena.korber@ndcls.ox.ac.uk",
         comment = c(ORCID = "0009-0005-3888-2648")),
  person(given = "Anand",
         family = "Mayakonda",
         role = c("aut"),
         email = "a.mayakonda@kitz-heidelberg.de"),
  person(given = "Maximilia",
         family = "Eggle",
         role = c("aut"),
         email = "maximilia.eggle@kitz-heidelberg.de"))
Description: This package provides modalities to analyze tumor evolution from whole genome sequencing data. In particular, it provides estimates of mutation densities at genomic segments and uses these to time the origin of the tumor. 
License: GPL (>= 3)
Copyright: Verena Körber, Anand Mayakonda, Maximilia Eggle (2025)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Depends: R (>= 4.3)
Imports: data.table, vcfR, tidyr, stats, utils, graphics, grDevices,
        ggplot2, gridExtra, survival, survminer, RColorBrewer,
        Biostrings
Suggests: BSgenome.Hsapiens.UCSC.hg19, BiocStyle, Cairo, rmarkdown,
        knitr, R.utils, tinytest, GenomeInfoDb, GenomicRanges, IRanges,
        MutationalPatterns, magick
biocViews: Software, StatisticalMethod, TimeCourse, Sequencing,
        WholeGenome, Survival, SomaticMutation
VignetteBuilder: knitr
RoxygenNote: 7.3.3
URL: https://github.com/VerenaK90/LACHESIS
BugReports: https://github.com/VerenaK90/LACHESIS/issues
git_url: https://git.bioconductor.org/packages/LACHESIS
git_branch: devel
git_last_commit: 1828e01
git_last_commit_date: 2026-03-16
Repository: Bioconductor 3.23
Date/Publication: 2026-03-16
NeedsCompilation: no
Packaged: 2026-03-16 20:23:52 UTC; biocbuild
Author: Verena Körber [aut, cre] (ORCID:
    <https://orcid.org/0009-0005-3888-2648>),
  Anand Mayakonda [aut],
  Maximilia Eggle [aut]
Maintainer: Verena Körber <verena.korber@ndcls.ox.ac.uk>
Built: R 4.6.0; ; 2026-03-17 01:13:53 UTC; unix
