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 such as Agilent SureSelect methyl-seq. It can potentially handle whole-genome bisulfite sequencing data if proper input format is provided.
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Genome Biol. 2012 Oct 3;13(10):R87. [Epub ahead of print]
methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles.
Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE.