Package: LACHESIS
Title: Functions used to analyze early tumor evolution from whole
        genome sequencing data
Version: 1.1.1
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
URL: https://github.com/VerenaK90/LACHESIS
BugReports: https://github.com/VerenaK90/LACHESIS/issues
Config/roxygen2/version: 8.0.0
RoxygenNote: 7.3.2
Config/pak/sysreqs: cmake make libicu-dev libjpeg-dev libpng-dev
        libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-07-22 14:44:51 UTC
RemoteUrl: https://github.com/bioc/LACHESIS
RemoteRef: HEAD
RemoteSha: 80e0065615dd44c436fede062ba96525c1994b69
NeedsCompilation: no
Packaged: 2026-10-20 08:43:25 UTC; root
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>