DMRcaller protocols

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
Stability Stable
Requirements GenomicRanges, IRanges, S4Vectors
Maintained Yes

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Documentation


Maintainers


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

Publication for DMRcaller

DMRcaller IN pipeline

2017
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, 2015). 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 […]

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