期刊
GENOME BIOLOGY
卷 13, 期 10, 页码 -出版社
BIOMED CENTRAL LTD
DOI: 10.1186/gb-2012-13-10-R87
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资金
- Leukemia & Lymphoma Society Special Fellow Award
- Doris Duke Clinical Scientist Development Award
- Sass Foundation Judah Folkman Fellowship
- LLS SCOR grant [7132-08]
- Burroughs Wellcome Clinical Translational Scientist Award
- Starr Cancer Consortium grant [I4-A442]
- National Institutes of Health [I4-A442, I4-A411, 1R01NS076465-01]
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.
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