title: 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.
authors.forename: Altuna
authors.initials: A
authors.lastname: Akalin
authors.forename: Matthias
authors.initials: M
authors.lastname: Kormaksson
authors.forename: Sheng
authors.initials: S
authors.lastname: Li
authors.forename: Francine E
authors.initials: FE
authors.lastname: Garrett-Bakelman
authors.forename: Maria E
authors.initials: ME
authors.lastname: Figueroa
authors.forename: Ari
authors.initials: A
authors.lastname: Melnick
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Mason
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D045744:Cell Line, Tumor; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D061986:MCF-7 Cells; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software