DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts

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DMRcaller : a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts. / Catoni, Marco; Tsang, Jonathan Mf; Greco, Alessandro P; Zabet, Nicolae Radu.

In: Nucleic Acids Research, 09.07.2018.

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@article{0068ec434fbe41b28a2f8414e0c40780,
title = "DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts",
abstract = "DNA methylation has been associated with transcriptional repression and detection of differential methylation is important in understanding the underlying causes of differential gene expression. Bisulfite-converted genomic DNA sequencing is the current gold standard in the field for building genome-wide maps at a base pair resolution of DNA methylation. Here we systematically investigate the underlying features of detecting differential DNA methylation in CpG and non-CpG contexts, considering both the case of mammalian systems and plants. In particular, we introduce DMRcaller, a highly efficient R/Bioconductor package, which implements several methods to detect differentially methylated regions (DMRs) between two samples. Most importantly, we show that different algorithms are required to compute DMRs and the most appropriate algorithm in each case depends on the sequence context and levels of methylation. Furthermore, we show that DMRcaller outperforms other available packages and we propose a new method to select the parameters for this tool and for other available tools. DMRcaller is a comprehensive tool for differential methylation analysis which displays high sensitivity and specificity for the detection of DMRs and performs entire genome wide analysis within a few hours.",
author = "Marco Catoni and Tsang, {Jonathan Mf} and Greco, {Alessandro P} and Zabet, {Nicolae Radu}",
year = "2018",
month = jul,
day = "9",
doi = "10.1093/nar/gky602",
language = "English",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",

}

RIS

TY - JOUR

T1 - DMRcaller

T2 - a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts

AU - Catoni, Marco

AU - Tsang, Jonathan Mf

AU - Greco, Alessandro P

AU - Zabet, Nicolae Radu

PY - 2018/7/9

Y1 - 2018/7/9

N2 - DNA methylation has been associated with transcriptional repression and detection of differential methylation is important in understanding the underlying causes of differential gene expression. Bisulfite-converted genomic DNA sequencing is the current gold standard in the field for building genome-wide maps at a base pair resolution of DNA methylation. Here we systematically investigate the underlying features of detecting differential DNA methylation in CpG and non-CpG contexts, considering both the case of mammalian systems and plants. In particular, we introduce DMRcaller, a highly efficient R/Bioconductor package, which implements several methods to detect differentially methylated regions (DMRs) between two samples. Most importantly, we show that different algorithms are required to compute DMRs and the most appropriate algorithm in each case depends on the sequence context and levels of methylation. Furthermore, we show that DMRcaller outperforms other available packages and we propose a new method to select the parameters for this tool and for other available tools. DMRcaller is a comprehensive tool for differential methylation analysis which displays high sensitivity and specificity for the detection of DMRs and performs entire genome wide analysis within a few hours.

AB - DNA methylation has been associated with transcriptional repression and detection of differential methylation is important in understanding the underlying causes of differential gene expression. Bisulfite-converted genomic DNA sequencing is the current gold standard in the field for building genome-wide maps at a base pair resolution of DNA methylation. Here we systematically investigate the underlying features of detecting differential DNA methylation in CpG and non-CpG contexts, considering both the case of mammalian systems and plants. In particular, we introduce DMRcaller, a highly efficient R/Bioconductor package, which implements several methods to detect differentially methylated regions (DMRs) between two samples. Most importantly, we show that different algorithms are required to compute DMRs and the most appropriate algorithm in each case depends on the sequence context and levels of methylation. Furthermore, we show that DMRcaller outperforms other available packages and we propose a new method to select the parameters for this tool and for other available tools. DMRcaller is a comprehensive tool for differential methylation analysis which displays high sensitivity and specificity for the detection of DMRs and performs entire genome wide analysis within a few hours.

U2 - 10.1093/nar/gky602

DO - 10.1093/nar/gky602

M3 - Article

C2 - 29986099

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

ER -