methcp is an R package for analyzing whole-genome bisulfite sequencing (WGBS) data. It implements MethCP algorithm introduced in (Gong and Purdom, 2018).
MethCP detects differentially methylated region for WGBS data based on change point detection, which naturally segments the genome and provide region-level differential analysis. It uses as input the results of a per-nucleotide test-statistic, like DSS or methylKit, and uses this input to segment the genome into regions. Then, several meta-analysis strategies are provided to identify which of those regions are DMR.
To install the package in R:
library(devtools)
install_github("boyinggong/methcp", dependencies=TRUE,
repos=BiocInstaller::biocinstallRepos())A tutorial can be found here.
Status Checks:
Contact: Boying Gong(boyinggong@berkeley.edu).