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: 2026-10-17 09:17:49 UTC; root
Repository: https://sarisworld.r-universe.dev
Date/Publication: 2026-05-29 15:10:02 UTC
RemoteUrl: https://github.com/cran/MethEvolSIM
RemoteRef: HEAD
RemoteSha: e4b141cbd0ebda0ddaa4de0ad2a96b4e8308208b
