MethylKit
methylKit is an R package for the analysis and annotation of DNA methylation data from high-throughput bisulfite sequencing experiments. It is designed for reduced representation bisulfite sequencing (RRBS) and related protocols, targeted capture approaches such as Agilent SureSelect Methyl-Seq, and base-resolution hydroxymethylation data generated with methods such as TAB-seq or oxBS-seq. Whole-genome bisulfite sequencing (WGBS) data are also supported through compatible input formats, including direct import of methylation calls from Bismark-aligned BAM files.
Key benefits
Comprehensive R-based workflow for DNA methylation analysis
Supports RRBS, targeted bisulfite sequencing, TAB-seq, oxBS-seq, and WGBS data
Handles base-pair resolution methylation and hydroxymethylation data
Enables quality assessment, coverage filtering, coverage normalization, and exploratory analysis
Supports identification of differentially methylated cytosines (DMCs) and regions (DMRs) between sample groups
Provides annotation and visualization functions for downstream interpretation
Available through Bioconductor and GitHub
Applications
Analysis of DNA methylation profiles from bisulfite sequencing
Identification of differentially methylated cytosines (DMCs) and regions (DMRs)
Comparative methylation analysis across conditions or sample groups
Analysis of 5hmC data from TAB-seq or oxBS-seq
Quality control and exploratory analysis of methylation datasets
Annotation of methylation changes with genomic features
Integration into reproducible R/Bioconductor workflows
Intended use
methylKit is intended for epigenetics researchers, molecular biologists, bioinformaticians, and computational biologists working with high-throughput bisulfite sequencing data. It is particularly suited for users who need an R-based, reproducible workflow for methylation analysis, differential methylation testing, and annotation of base-resolution methylation data.
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