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

doi:10.1186/gb-2012-13-10-R87

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

Human Genetics

Research output: Contribution to journal › Article › peer-review

584 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 language	English (US)
Article number	R87
Journal	Genome biology
Volume	13
Issue number	10
DOIs	https://doi.org/10.1186/gb-2012-13-10-R87
State	Published - Oct 3 2012

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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10.1186/gb-2012-13-10-R87

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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.",

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