MethylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E. Garrett-Bakelman, Maria E. Figueroa, Ari Melnick, Christopher E. Mason

Research output: Contribution to journalArticle

497 Scopus citations

Abstract

DNA methylation is a chemical modification of cytosine bases that is pivotal for gene regulation,cellular specification and cancer development. Here, we describe an R package, methylKit, thatrapidly analyzes genome-wide cytosine epigenetic profiles from high-throughput methylation andhydroxymethylation sequencing experiments. methylKit includes functions for clustering, samplequality visualization, differential methylation analysis and annotation features, thus automatingand simplifying many of the steps for discerning statistically significant bases or regions of DNAmethylation. Finally, we demonstrate methylKit on breast cancer data, in which we find statisticallysignificant regions of differential methylation and stratify tumor subtypes. methylKit is availableat http://code.google.com/p/methylkit.

Original languageEnglish (US)
Article numberR87
JournalGenome biology
Volume13
Issue number10
DOIs
StatePublished - Oct 3 2012

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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    Akalin, A., Kormaksson, M., Li, S., Garrett-Bakelman, F. E., Figueroa, M. E., Melnick, A., & Mason, C. E. (2012). MethylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome biology, 13(10), [R87]. https://doi.org/10.1186/gb-2012-13-10-R87