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, thatrapidly analyzes genome-wide cytosine epigenetic profiles from high-throughput methylation andhydroxymethylation sequencing experiments. methylKit includes functions for clustering, samplequality visualization, differential methylation analysis and annotation features, thus automatingand simplifying many of the steps for discerning statistically significant bases or regions of DNAmethylation. Finally, we demonstrate methylKit on breast cancer data, in which we find statisticallysignificant regions of differential methylation and stratify tumor subtypes. methylKit is availableat http://code.google.com/p/methylkit.
| Original language | English (US) |
|---|---|
| Article number | R87 |
| Journal | Genome Biology |
| Volume | 13 |
| Issue number | 10 |
| DOIs | |
| State | Published - Oct 3 2012 |
| Externally published | Yes |
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ASJC Scopus subject areas
- Ecology, Evolution, Behavior and Systematics
- Genetics
- Cell Biology
Cite this
MethylKit : a comprehensive R package for the analysis of genome-wide DNA methylation profiles. / Akalin, Altuna; Kormaksson, Matthias; Li, Sheng; Garrett-Bakelman, Francine E.; Figueroa, Maria; Melnick, Ari; Mason, Christopher E.
In: Genome Biology, Vol. 13, No. 10, R87, 03.10.2012.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - MethylKit
T2 - a comprehensive R package for the analysis of genome-wide DNA methylation profiles
AU - Akalin, Altuna
AU - Kormaksson, Matthias
AU - Li, Sheng
AU - Garrett-Bakelman, Francine E.
AU - Figueroa, Maria
AU - Melnick, Ari
AU - Mason, Christopher E.
PY - 2012/10/3
Y1 - 2012/10/3
N2 - 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, thatrapidly analyzes genome-wide cytosine epigenetic profiles from high-throughput methylation andhydroxymethylation sequencing experiments. methylKit includes functions for clustering, samplequality visualization, differential methylation analysis and annotation features, thus automatingand simplifying many of the steps for discerning statistically significant bases or regions of DNAmethylation. Finally, we demonstrate methylKit on breast cancer data, in which we find statisticallysignificant regions of differential methylation and stratify tumor subtypes. methylKit is availableat http://code.google.com/p/methylkit.
AB - 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, thatrapidly analyzes genome-wide cytosine epigenetic profiles from high-throughput methylation andhydroxymethylation sequencing experiments. methylKit includes functions for clustering, samplequality visualization, differential methylation analysis and annotation features, thus automatingand simplifying many of the steps for discerning statistically significant bases or regions of DNAmethylation. Finally, we demonstrate methylKit on breast cancer data, in which we find statisticallysignificant regions of differential methylation and stratify tumor subtypes. methylKit is availableat http://code.google.com/p/methylkit.
UR - http://www.scopus.com/inward/record.url?scp=84866860221&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84866860221&partnerID=8YFLogxK
U2 - 10.1186/gb-2012-13-10-R87
DO - 10.1186/gb-2012-13-10-R87
M3 - Article
C2 - 23034086
AN - SCOPUS:84866860221
VL - 13
JO - Genome Biology
JF - Genome Biology
SN - 1465-6914
IS - 10
M1 - R87
ER -