vmrseq: Detecting variably methylated regions (VMRs) from single-cell bisulfite sequencing

The R package vmrseq is a novel computational tool developed for pinpointing variably methylated regions (VMRs) in scBS-seq data without prior knowledge on size or location. High-throughput single-cell measurements of DNA methylation allows studying inter-cellular epigenetic heterogeneity, but this task faces the challenges of sparsity and noise. vmrseq overcomes these challenges and identifies variably methylated regions accurately and robustly.

Installation

You can install the development version of vmrseq from GitHub with:

# install.packages("devtools")
devtools::install_github("nshen7/vmrseq")

Online Vignette

An online vignette of how to use the vmrseq package can be found at https://rpubs.com/nshen7/vmrseq-vignette

Citation

Ning Shen and Keegan Korthauer. 2023. “Vmrseq: Probabilistic Modeling of Single-Cell Methylation Heterogeneity.” bioRxiv. https://doi.org/10.1101/2023.11.20.567911.

License/Copyright

This package is made available under an MIT license.