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MethEvolSIM  

Simulate DNA Methylation Dynamics on Different Genomic Structures along Genealogies
View on CRAN: Click here


Download and install MethEvolSIM package within the R console
Install from CRAN:
install.packages("MethEvolSIM")

Install from Github:
library("remotes")
install_github("cran/MethEvolSIM")

Install by package version:
library("remotes")
install_version("MethEvolSIM", "0.1.7")



Attach the package and use:
library("MethEvolSIM")
Maintained by
Sara Castillo Vicente
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2024-04-18
Latest Update: 2024-04-18
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.
How to cite:
Sara Castillo Vicente (2024). MethEvolSIM: Simulate DNA Methylation Dynamics on Different Genomic Structures along Genealogies. R package version 0.1.7, https://cran.r-project.org/web/packages/MethEvolSIM. Accessed 03 Jan. 2025.
Previous versions and publish date:
0.1.1 (2024-04-30 13:30), 0.1.2 (2024-05-24 14:40), 0.1.3 (2024-07-20 08:00), 0.1.4 (2024-07-30 10:30), 0.1.5 (2024-08-16 14:20), 0.1.6 (2024-09-09 17:10), 0.1 (2024-04-18 16:12)
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Complete documentation for MethEvolSIM
Functions, R codes and Examples using the MethEvolSIM R package
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