Format

Send to

Choose Destination
Genome Biol. 2012 Oct 3;13(10):R87. doi: 10.1186/gb-2012-13-10-r87.

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

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, that rapidly analyzes genome-wide cytosine epigenetic profiles from high-throughput methylation and hydroxymethylation sequencing experiments. methylKit includes functions for clustering, sample quality visualization, differential methylation analysis and annotation features, thus automating and simplifying many of the steps for discerning statistically significant bases or regions of DNA methylation. Finally, we demonstrate methylKit on breast cancer data, in which we find statistically significant regions of differential methylation and stratify tumor subtypes. methylKit is available at http://code.google.com/p/methylkit.

PMID:
23034086
PMCID:
PMC3491415
DOI:
10.1186/gb-2012-13-10-r87
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center