Package: MethEvolSIM 0.1.5
MethEvolSIM: Simulate DNA Methylation Dynamics on Different Genomic Structures along Genealogies
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.
Authors:
MethEvolSIM_0.1.5.tar.gz
MethEvolSIM_0.1.5.tar.gz(r-4.5-noble)MethEvolSIM_0.1.5.tar.gz(r-4.4-noble)
MethEvolSIM_0.1.5.tgz(r-4.4-emscripten)MethEvolSIM_0.1.5.tgz(r-4.3-emscripten)
MethEvolSIM.pdf |MethEvolSIM.html✨
MethEvolSIM/json (API)
# Install 'MethEvolSIM' in R: |
install.packages('MethEvolSIM', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 22 days agofrom:a4dd8bff3d. Checks:OK: 2. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 20 2024 |
R-4.5-linux | OK | Aug 20 2024 |
Exports:get_parameterValuessimulate_evolDatasimulate_initialData
Dependencies:R6
Readme and manuals
Help Manual
Help page | Topics |
---|---|
combiStructureGenerator | combiStructureGenerator |
Get Default Parameter Values | get_parameterValues |
Simulate Data Evolution along a Tree | simulate_evolData |
Simulate Initial Data | simulate_initialData |
singleStructureGenerator | singleStructureGenerator |
treeMultiRegionSimulator | treeMultiRegionSimulator |