Efficient detection of differentially methylated regions using DiMmeR
نویسندگان
چکیده
منابع مشابه
Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions
Analysis of bisulfite sequencing data usually requires two tasks: to call methylated cytosines (mCs) in a sample, and to detect differentially methylated regions (DMRs) between paired samples. Although numerous tools have been proposed for mC calling, methods for DMR detection have been largely limited. Here, we present Bisulfighter, a new software package for detecting mCs and DMRs from bisulf...
متن کاملIdentification of differentially methylated regions (DMRs) of neuronatin in mice
BACKGROUND Neuronatin (NNAT) is a paternal-inherited imprinted gene, first discovered in the rat neonatal brain, where it plays vital roles for neuronal growth, brain development, and metabolic regulation. The maternal imprint of NNAT has been identified in mice; however, the differentially methylated regions (DMRs) involved in the monoallelic expression of NNAT have not yet been investigated. ...
متن کاملDetection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates
DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Recent developments in whole genome bisulfite sequencing (WGBS) technology have enabled genome-wide measurements of DNA methylation at single base pair resolution. Many experiments have been conducted to compare DNA methylation profiles under different biological contexts, with the goal o...
متن کاملDetection of significantly differentially methylated regions in targeted bisulfite sequencing data
MOTIVATION Bisulfite sequencing is currently the gold standard to obtain genome-wide DNA methylation profiles in eukaryotes. In contrast to the rapid development of appropriate pre-processing and alignment software, methods for analyzing the resulting methylation profiles are relatively limited so far. For instance, an appropriate pipeline to detect DNA methylation differences between cancer an...
متن کاملDetection and accurate false discovery rate control of differentially methylated regions from whole genome bisulfite sequencing.
With recent advances in sequencing technology, it is now feasible to measure DNA methylation at tens of millions of sites across the entire genome. In most applications, biologists are interested in detecting differentially methylated regions, composed of multiple sites with differing methylation levels among populations. However, current computational approaches for detecting such regions do n...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2016
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btw657