Package: RAMEN
Title: Regional Association of Methylome variability with the Exposome
        and geNome
Version: 2.99.4
Authors@R: c(
    person("Erick I.", "Navarro-Delgado", 
            email = "erick.delgado@ubc.ca", 
            role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-1040-3519")),
    person("Keegan", "Korthauer", 
            role = "aut", 
            email = "keegan@stat.ubc.ca", 
            comment = c(ORCID = "0000-0002-4565-1654")),
    person("Michael S.", "Kobor", 
            email = "michael.kobor@ubc.ca",
            role = "aut",
            comment = c(ORCID = "0000-0003-4140-1743")),
    person("Lluís", "Revilla Sancho", 
            email = "lluis.revilla@gmail.com",
            role = "rev",
            comment = c(ORCID = "0000-0001-9747-2570")),
    person("Ulduz", "Vafadarshamasbi", 
            email = "vafadar.u@uq.edu.au",
            role = "rev",
            comment = c(ORCID = "0000-0002-8370-8084")),
    person("The University of British Columbia", role = "fnd")
            )
Description: RAMEN is an R package which goal is to identify Variable Methylated Loci (VML) in microarray DNA methylation data. Then, using genome and exposome data, RAMEN identifies which individual genetic (G) or environmental (E) or joint (G+E or GxE) model better explains the VML variability. This package provides estimates of genetic and environmental contribution for each VML, allowing researchers to gain insights into the complex interplay between genetics, environment and DNA methylation.
License: GPL (>= 3)
Encoding: UTF-8
biocViews: DNAMethylation, GenomeWideAssociation, Epigenetics,
        Regression, SNP, Microarray, MethylationArray,
        GeneticVariability
Roxygen: list(markdown = TRUE)
Suggests: BiocStyle, knitr, magick, rmarkdown, ggplot2, tidyr,
        doParallel, IlluminaHumanMethylation450kanno.ilmn12.hg19,
        IlluminaHumanMethylationEPICv2anno.20a1.hg38, testthat (>=
        3.0.0)
Config/testthat/edition: 3
Imports: doRNG, dplyr, foreach, GenomicRanges, glmnet, IRanges,
        matrixStats, methods, relaimpo, S4Vectors,
        IlluminaHumanMethylationEPICanno.ilm10b4.hg19, stats
VignetteBuilder: knitr
Depends: R (>= 4.6.0)
LazyData: true
URL: https://ropensci.github.io/RAMEN/ ,
        https://github.com/ropensci/RAMEN/
BugReports: https://github.com/ropensci/RAMEN/issues
Config/roxygen2/version: 8.1.1
git_url: https://git.bioconductor.org/packages/RAMEN
git_branch: devel
git_last_commit: 3cdc9ca
git_last_commit_date: 2026-10-21
Repository: Bioconductor 3.24
Date/Publication: 2026-10-22
NeedsCompilation: no
Packaged: 2026-10-22 22:31:26 UTC; biocbuild
Author: Erick I. Navarro-Delgado [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1040-3519>),
  Keegan Korthauer [aut] (ORCID: <https://orcid.org/0000-0002-4565-1654>),
  Michael S. Kobor [aut] (ORCID: <https://orcid.org/0000-0003-4140-1743>),
  Lluís Revilla Sancho [rev] (ORCID:
    <https://orcid.org/0000-0001-9747-2570>),
  Ulduz Vafadarshamasbi [rev] (ORCID:
    <https://orcid.org/0000-0002-8370-8084>),
  The University of British Columbia [fnd]
Maintainer: Erick I. Navarro-Delgado <erick.delgado@ubc.ca>
Built: R 4.6.1; ; 2026-10-23 12:56:42 UTC; unix
