methylKit

DNA methylation analysis from high-throughput bisulfite sequencing results

Bioconductor version: 3.23 · Package version: 1.38.0

methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Methylation calling can be performed directly from Bismark aligned BAM files.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("methylKit")