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
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://ropensci.r-universe.dev
Date/Publication: 2026-10-21 21:31:00 UTC
RemoteUrl: https://github.com/ropensci/RAMEN
RemoteRef: main
RemoteSha: 3cdc9cab1a4ca5d07d965619ace4c7dac7dcb4a7
NeedsCompilation: no
Packaged: 2026-10-22 00:29:21 UTC; root
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>