Package: coMethDMR
Title: Accurate identification of co-methylated and differentially
        methylated regions in epigenome-wide association studies
Version: 1.16.0
Authors@R: c(
  person("Fernanda", "Veitzman", email = "fveit001@fiu.edu", role = c("cre")),
  person("Lissette", "Gomez", email = "lxg255@miami.edu", role = c("aut")),
  person("Tiago", "Silva", email = "txs902@med.miami.edu", role = c("aut")),
  person("Ning", "Lijiao", role = c("ctb")),
  person("Boissel", "Mathilde", role = c("ctb")),
  person("Lily", "Wang", email = "lily.wang@med.miami.edu", role = c("aut")),
  person("Gabriel", "Odom", email = "gabriel.odom@fiu.edu", role = c("aut"))
  )
Description: 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.
Depends: R (>= 4.1)
License: GPL-3
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.1.2
Imports: AnnotationHub, BiocParallel, bumphunter, ExperimentHub,
        GenomicRanges, IRanges, lmerTest, methods, stats, utils
Suggests: BiocStyle, corrplot, knitr, rmarkdown, testthat,
        IlluminaHumanMethylation450kanno.ilmn12.hg19,
        IlluminaHumanMethylationEPICanno.ilm10b4.hg19
biocViews: DNAMethylation, Epigenetics, MethylationArray,
        DifferentialMethylation, GenomeWideAssociation
VignetteBuilder: knitr
BugReports: https://github.com/TransBioInfoLab/coMethDMR/issues
URL: https://github.com/TransBioInfoLab/coMethDMR
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:57:35 UTC
RemoteUrl: https://github.com/bioc/coMethDMR
RemoteRef: RELEASE_3_23
RemoteSha: 6ff4a30f75cd2275e98aa0234305954a0b41732a
NeedsCompilation: no
Packaged: 2026-05-04 09:39:31 UTC; root
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@fiu.edu>
Built: R 4.6.0; ; 2026-05-04 10:01:53 UTC; windows
