ArticleNucleic acids research2018
DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed.
- Article
- Methylthioadenosine-driven rewiring of sulfur assimilation lowers the methyl index and fertility in Arabidopsis.Journal of experimental botany · 2026Article
- Genome-Wide Analysis of DNA Methylation Profiles on Jining Grey Goat Uterus Associated with Prolificacy Using Whole-Genome Bisulfite Sequencing.Animals : an open access journal from MDPI · 2026Article
- TET2 loss triggers ssDNA gap accumulation and heightened PARP inhibitor sensitivity.Nature communications · 2026Article
- DiffMethylTools: a toolbox for the detection, annotation, and visualization of differential methylation.Life science alliance · 2026Article
- MultiDMPcaller: a one-stop software for detection and visualization of differentially methylated positions and regions.Bioinformatics (Oxford, England) · 2026Article
- Article
- Methionine overaccumulation reinforces heterochromatic non-CG hypermethylation and transposon silencing in Arabidopsis.Plant physiology · 2026Article
- Allele-specific methylation ofScience advances · 2026Article
- Detection of differential DNA methylation in date palm (Phoenix dactylifera L.) vitroplants using whole genome bisulfite sequencing analysis.BMC plant biology · 2026Article
- cyberDMR: accurate and robust identification of differentially methylated regions from WGS-derived methylomes.BMC biology · 2026Article
- Heterochromatin reorganization associated with the transcriptional reprogramming under viral infection in Arabidopsis.Nucleic acids research · 2026Article
- Gene body methylation buffers noise in gene expression in plants.Nucleic acids research · 2026Article
- Aging drives a program of DNA methylation decay in plant organs.Science (New York, N.Y.) · 2026Article
- 24-nt-phasiRNA associated CHG/CHH DNA methylation contributes to growth heterosis ofForestry research · 2026Article
- Genotype-dependent DNA methylation patterns are negatively associated with allelic variation rather than heat-induced gene expression in two contrasting potato genotypes.The Plant journal : for cell and molecular biology · 2026Article
- Multi-dimensional epigenomic dynamics converge on H3K4-mediated regulation of low-COPlant communications · 2025Article
- DNA methylation contributes to plant acclimation to naturally fluctuating light.The New phytologist · 2025Article
- DNA methylation and machine learning: challenges and perspective toward enhanced clinical diagnostics.Clinical epigenetics · 2025Review
- Non-CG DNA methylation in animal genomes.Nature genetics · 2025Review
9 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
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.
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Registered trials
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