Other packages > Find by keyword >

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", "0.2.1")



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: 2025-04-11
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 0.2.1, https://cran.r-project.org/web/packages/MethEvolSIM. Accessed 06 Mar. 2026.
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), 0.1.7 (2024-09-22 10:20), 0.1 (2024-04-18 16:12), 0.2 (2025-03-17 08:00)
Other packages that cited MethEvolSIM R package
View MethEvolSIM citation profile
Other R packages that MethEvolSIM depends, imports, suggests or enhances
Complete documentation for MethEvolSIM
Functions, R codes and Examples using the MethEvolSIM R package
Full MethEvolSIM package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
DatabionicSwarm  
Swarm Intelligence for Self-Organized Clustering
Algorithms implementing populations of agents that interact with one another and sense their environ ...
Download / Learn more Package Citations See dependency  
openxlsx  
Read, Write and Edit xlsx Files
Simplifies the creation of Excel .xlsx files by providing a high level interface to writing, stylin ...
Download / Learn more Package Citations See dependency  
mlr3viz  
Visualizations for 'mlr3'
Visualization package of the 'mlr3' ecosystem. It features plots for mlr3 objects such as tasks, le ...
Download / Learn more Package Citations See dependency  
solitude  
An Implementation of Isolation Forest
Isolation forest is anomaly detection method introduced by the paper Isolation based Anomaly Detecti ...
Download / Learn more Package Citations See dependency  
lbfgs  
Limited-memory BFGS Optimization
A wrapper built around the libLBFGS optimization library by Naoaki Okazaki. The lbfgs package implem ...
Download / Learn more Package Citations See dependency  

26,264

R Packages

223,360

Dependencies

70,244

Author Associations

26,265

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA