DMRcaller statistics

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Citations per year

Number of citations per year for the bioinformatics software tool DMRcaller
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Tool usage distribution map

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

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Popular tool citations

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DMRcaller specifications

Information


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
Requirements
parallel, BiocGenerics, IRanges, GenomicRanges, S4Vectors, Rcpp, RUnit, knitr, R(>=3.2), RcppRoll
Maintained Yes

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Versioning


No version available

Documentation


Maintainers


  • person_outline Nicolae Zabet
  • person_outline Jonathan Tsang

Publication for DMRcaller

DMRcaller citations

 (4)
library_books

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

2018
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 […]

library_books

DNA sequence properties that predict susceptibility to epiallelic switching

2017
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 […]

library_books

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

2017
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 […]

call_split

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

2016
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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