DMRcaller protocols

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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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Maintainers


  • person_outline Nicolae Zabet <>
  • person_outline Jonathan Tsang <>

Publication for DMRcaller

DMRcaller in pipeline

2016
PMCID: 5167412
PMID: 27992519
DOI: 10.1371/journal.pone.0168623

[…] 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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DMRcaller in publications

 (4)
PMCID: 5917015
PMID: 29725341
DOI: 10.3389/fpls.2018.00497

[…] of bowtie as short read mapper. after alignment, bs-seeker2 was used to call methylation levels from the mapping results using the default settings., the methylation information was then used in dmrcaller () provided by bioconductor to determine differentially methylated regions (dmrs) and visualize methylation level distribution over whole chromosomes. the methylation levels determined […]

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

[…] 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 […]

PMCID: 5397141
PMID: 28053115
DOI: 10.1093/nar/gkw1330

[…] and confirmed that regions that gain cphpg methylation in the second generation of ibm1 mutant () completely include the dmbs detected in the first generation of ibm1 ()., 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 […]

PMCID: 5167412
PMID: 27992519
DOI: 10.1371/journal.pone.0168623

[…] 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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