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

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Item Type:Article
Title:methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles
Creators Name:Akalin, A. and Kormaksson, M. and Li, S. and Garrett-Bakelman, F.E. and Figueroa, M.E. and Melnick, A. and Mason, C.E.
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.
Keywords:Breast Neoplasms, Tumor Cell Line, DNA Methylation, DNA Sequence Analysis, Genetic Epigenesis, Genomics, High-Throughput Nucleotide Sequencing, Human Genome, MCF-7 Cells, Software
Source:Genome Biology
ISSN:1474-7596
Publisher:BioMed Central (U.K.)
Volume:13
Number:10
Page Range:R87
Date:3 October 2012
Official Publication:https://doi.org/10.1186/gb-2012-13-10-r87
PubMed:View item in PubMed

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