articleGenome biologyOct 3, 2012GOLD OA

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

AAAltuna AkalinMKMatthías KormákssonSLSheng LiFEFrancine E. Garrett-BakelmanMEMaría E. Figueroa

Cornell University · University of Michigan

PubMed
Indexed incrossrefdoajpubmed

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…

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Topics & keywords

Topics
Keywords
  • Biology
  • DNA methylation
  • Methylation
  • Computational biology
  • Epigenetics
  • Genome
  • Genetics
  • Epigenomics
UN Sustainable Development Goals
  • Good health and well-being
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