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.
| Version: | 0.2 |
| Depends: | R (≥ 4.0) |
| Imports: | R6, ape |
| Suggests: | knitr, rmarkdown, testthat (≥ 3.0.0) |
| Published: | 2025-03-17 |
| DOI: | 10.32614/CRAN.package.MethEvolSIM |
| Author: | Sara Castillo Vicente [aut, cre], Dirk Metzler [aut, ths] |
| Maintainer: | Sara Castillo Vicente <castillo at bio.lmu.de> |
| License: | GPL (≥ 3) |
| NeedsCompilation: | no |
| Materials: | README |
| CRAN checks: | MethEvolSIM results [issues need fixing before 2025-03-31] |
| Reference manual: | MethEvolSIM.pdf |
| Vignettes: |
CFTP Method (source, R code) Introduction to MethEvolSIM (source, R code) Summary Statistics with MethEvolSIM (source, R code) |
| Package source: | MethEvolSIM_0.2.tar.gz |
| Windows binaries: | r-devel: MethEvolSIM_0.2.zip, r-release: MethEvolSIM_0.2.zip, r-oldrel: MethEvolSIM_0.1.7.zip |
| macOS binaries: | r-devel (arm64): MethEvolSIM_0.1.7.tgz, r-release (arm64): MethEvolSIM_0.1.7.tgz, r-oldrel (arm64): MethEvolSIM_0.1.7.tgz, r-devel (x86_64): MethEvolSIM_0.2.tgz, r-release (x86_64): MethEvolSIM_0.2.tgz, r-oldrel (x86_64): MethEvolSIM_0.2.tgz |
| Old sources: | MethEvolSIM archive |
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