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An R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. methylKit is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent SureSelect methyl-seq. In addition, methylKit can deal with base-pair resolution data for 5hmC obtained from Tab-seq or oxBS-seq. It can also handle whole-genome bisulfite sequencing data if proper input format is provided.

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methylKit classification

methylKit specifications

Software type:
Restrictions to use:
Output format:
Bedgraph, tab-delimited text, images
Programming languages:
Computer skills:
Command line interface
Input format:
Tab-delimited text
Operating system:
Unix/Linux, Mac OS, Windows
GNU General Public License version 2.0

methylKit distribution


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methylKit support



  • Christopher E. Mason <>


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Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY USA; Department of Public Health, Weill Cornell Medical College, New York, NY, USA; Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medical College, New York, NY, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA

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