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This is the development version of coMethDMR; for the stable release version, see coMethDMR.

Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies

Bioconductor version: Development (3.19)

coMethDMR identifies genomic regions associated with continuous phenotypes by optimally leverages covariations among CpGs within predefined genomic regions. Instead of testing all CpGs within a genomic region, coMethDMR carries out an additional step that selects co-methylated sub-regions first without using any outcome information. Next, coMethDMR tests association between methylation within the sub-region and continuous phenotype using a random coefficient mixed effects model, which models both variations between CpG sites within the region and differential methylation simultaneously.

Author: Fernanda Veitzman [cre], Lissette Gomez [aut], Tiago Silva [aut], Ning Lijiao [ctb], Boissel Mathilde [ctb], Lily Wang [aut], Gabriel Odom [aut]

Maintainer: Fernanda Veitzman <fveit001 at fiu.edu>

Citation (from within R, enter citation("coMethDMR")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

coMethDMR with Parallel Computing HTML R Script
Introduction to coMethDMR HTML R Script
Reference Manual PDF


biocViews DNAMethylation, DifferentialMethylation, Epigenetics, GenomeWideAssociation, MethylationArray, Software
Version 1.7.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-3
Depends R (>= 4.1)
Imports AnnotationHub, BiocParallel, bumphunter, ExperimentHub, GenomicRanges, IRanges, lmerTest, methods, stats, utils
System Requirements
URL https://github.com/TransBioInfoLab/coMethDMR
Bug Reports https://github.com/TransBioInfoLab/coMethDMR/issues
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Suggests BiocStyle, corrplot, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19
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Source Package coMethDMR_1.7.0.tar.gz
Windows Binary coMethDMR_1.7.0.zip
macOS Binary (x86_64) coMethDMR_1.7.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/coMethDMR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/coMethDMR
Bioc Package Browser https://code.bioconductor.org/browse/coMethDMR/
Package Short Url https://bioconductor.org/packages/coMethDMR/
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