Software and tools
Mixed model Association for Count data via Augmentation from Lea, Tung, and Zhou
MACAU (binomial mixed model with kinship/population structure controls, for bisulfite sequencing studies) is maintained by our collaborator Xiang Zhou (University of Michigan Biostatistics). You can download the software and user manual here.
Bisulfite sequencing simulator/power analysis (R Shiny app from Lea et al, forthcoming)
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, A.J., Vilgalys, T.P., Durst, P.A.P., and Tung, J. Maximizing ecological and evolutionary insight from bisulfite sequencing data sets. bioRxiv: dx.doi.org/10.1101/091488
Tung lab reduced representation bisulfite sequencing (RRBS) protocol