GitHub - nshen7/vmrseq: An R package for detecting cell-to-cell variably methylated regions (VMRs) from single-cell bisulfite sequencing leveraging probabilistic models. (original) (raw)
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
in R from Bioconductor (recommended) or GitHub with:
Install stable version from Bioconductor
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("vmrseq")
Or development version from Github
install.packages("remotes")
remotes::install_github("nshen7/vmrseq")
Online Vignette
- An online vignette of 'Get Started' on the
vmrseq
package can be found athttps://rpubs.com/nshen7/vmrseq-vignette. - An example workflow on scBS-seq data analysis using
vmrseq
can be found athttps://github.com/nshen7/vmrseq-workflow-vignette.
Docker Image
We provide a Docker image for robust setup and use of this package. The Docker image includes all necessary dependencies for the package and vignettes. To pull the Docker image from Docker Hub, use the following command in bash:
docker pull nshen7/vmrseq-bioc-3.19:latest
Citation
Shen, N., Korthauer, K. vmrseq: probabilistic modeling of single-cell methylation heterogeneity. Genome Biol 25, 321 (2024). https://doi.org/10.1186/s13059-024-03457-7