Bisulfite sequencing simulator/power analysis (R shiny app from Lea, et al. 2017)
This R shiny app interactively simulates bisulfite sequencing read counts and performs power analysis using a variety of common modeling approaches for DNA methylation analysis. You can download the app, example input files, and instructions here, or the instructions/readme file on its own here.
If you use this app in published work, please cite: Lea AJ, Vilgalys TPV, Durst PAP, and Tung J. 2017. Maximizing ecological and evolutionary insight from bisulfite sequencing data sets. Nature Ecology and Evolution 1(8): 1074.
Code in this repository simulates the trait evolution under Ornstein-Uhlenbeck models with user-defined parameters and fits evolutionary models of phenotypic drift, stabilizing selection, and positive selection. You can download these scripts and example files from github.com/TaurVil/PapioMethylation.
If you use this app in published work, please cite: Vilgalys TP, Rogers J, Jolly C, Baboon Genome Analysis Consortium, Mukherjee S, and Tung J. 2018. Evolution of DNA methylation in Papio baboons. bioRxiv: dx.doi.org/10.1101/400093