DMRcaller statistics

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Citations per year

Number of citations per year for the bioinformatics software tool DMRcaller

Tool usage distribution map

This map represents all the scientific publications referring to DMRcaller per scientific context
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DMRcaller specifications


Unique identifier OMICS_19198
Name DMRcaller
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The CX report files produced by Bismark.
Output data A list of DMRs stored as GRanges objects.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.0
Stability Stable
parallel, BiocGenerics, IRanges, GenomicRanges, S4Vectors, Rcpp, RUnit, knitr, R(>=3.2), RcppRoll
Maintained Yes




No version available



  • person_outline Nicolae Zabet
  • person_outline Jonathan Tsang

Publication for DMRcaller

DMRcaller citations


Massive Loss of DNA Methylation in Nitrogen , but Not in Phosphorus Deficient Zea mays Roots Is Poorly Correlated With Gene Expression Differences

Front Plant Sci
PMCID: 5917015
PMID: 29725341
DOI: 10.3389/fpls.2018.00497

[…] (1.29%, Figure ). Whether the methylation changes were distributed uniformly across chromosomes was analyzed by low-resolution profiles of average methylation levels in a grid of 5 million bases via DMRcaller (Figure ). As a representative, chromosome 1 methylation is shown for the three different cytosine contexts and control, -N and -P conditions. As for the general methylation levels, a rather […]


DNA sequence properties that predict susceptibility to epiallelic switching

PMCID: 5331756
PMID: 28069706
DOI: 10.15252/embj.201695602

[…] l number of reads and c is the conversion rate). DMRs (differentially methylated regions) were defined comparing methylation in wild‐type Col‐0 with the other conditions analysed using the R package “DMRcaller” (Zabet & Tsang, ). We used “noise filter” method to compute CpG and CpHpG DMRs. Briefly, the “noise filter” method uses a triangular kernel to smooth the total number of reads and the total […]


Cytosine methylation at CpCpG sites triggers accumulation of non CpG methylation in gene bodies

Nucleic Acids Res
PMCID: 5397141
PMID: 28053115
DOI: 10.1093/nar/gkw1330

[…] To compute DMBs we used DMRcaller (), which is an R/Bioconductor package (,). Briefly, we considered 100-bp tilling bins and performed a Score test (leading to results similar to a Fisher's exact test) between methylated and […]


Site Dependent Differences in DNA Methylation and Their Impact on Plant Establishment and Phosphorus Nutrition in Populus trichocarpa

PLoS One
PMCID: 5167412
PMID: 27992519
DOI: 10.1371/journal.pone.0168623
call_split See protocol

[…] a: p = 1 –(# methylated cytosines) / (# of cytosines) [,] and amounted 99.17% (Anderlingen) and 99.11% (Wallstawe). Methylation distribution along single chromosomes was displayed with Bioconductor’s DMRcaller. Methylation levels around annotated transcriptional starting sites were identified using the R project for statistical computing. In addition, BS-derived differentially methylated regions ( […]

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