Package: MethEvolSIM
Title: Simulate DNA Methylation Dynamics on Different Genomic
        Structures along Genealogies
Version: 0.3.0
Authors@R: c(
    person('Sara', 'Castillo Vicente', , 'castillo@bio.lmu.de', role=c('aut', 'cre')),
    person('Dirk', 'Metzler', , 'metzler@bio.lmu.de', role=c('aut', 'ths'))
    )
Author: Sara Castillo Vicente [aut, cre],
  Dirk Metzler [aut, ths]
Maintainer: Sara Castillo Vicente <castillo@bio.lmu.de>
Description: DNA methylation is an epigenetic modification involved in genomic stability,
      gene regulation, development and disease.
      DNA methylation occurs mainly through the addition of a methyl group to cytosines, 
      for example to cytosines in a CpG dinucleotide context (CpG stands for a cytosine followed by a guanine).
      Tissue-specific methylation patterns lead to genomic regions with different characteristic
      methylation levels.
      E.g. in vertebrates CpG islands (regions with high CpG content) that are associated to promoter regions of
      expressed genes tend to be unmethylated.
      'MethEvolSIM' is a model-based simulation software for the generation and modification
      of cytosine methylation patterns along a given tree, which can be a genealogy of
      cells within an organism, a coalescent tree of DNA sequences sampled from a population, or a species tree.
      The simulations are based on an extension of the model of
      Grosser & Metzler (2020) <doi:10.1186/s12859-020-3438-5> and allows for changes of
      the methylation states at single cytosine positions as well as simultaneous changes of methylation
      frequencies in genomic structures like CpG islands.
License: GPL (>= 3)
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Config/testthat/edition: 3
Imports: R6, ape
Depends: R (>= 4.0)
VignetteBuilder: knitr
Config/roxygen2/version: 8.0.0
NeedsCompilation: no
Packaged: 2026-05-29 14:20:12 UTC; castillo
Repository: CRAN
Date/Publication: 2026-05-29 15:10:02 UTC
Built: R 4.6.1; ; 2026-07-02 02:29:54 UTC; windows
