Submitting Author Name: Erick I. Navarro-Delgado
Submitting Author Github Handle: @ErickNavarroD
Repository: https://github.com/ErickNavarroD/RAMEN/tree/ropensci-software-review
Version submitted: 2.0.0
Submission type: Standard
Editor: @maurolepore
Reviewers: TBD

Archive: TBD
Version accepted: TBD
Language: en

• Paste the full DESCRIPTION file inside a code block below:

Package: RAMEN
Title: RAMEN: Regional Association of Methylome variability with the Exposome and geNome
Version: 2.0.0
Authors@R: 
    person("Erick I.", "Navarro-Delgado", , "ericknadel98@hotmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-1040-3519"))
Description: R package that identifies which genetic (G), environmental (E), additive (G+E) or interaction (GxE) effect better explains DNA methylation levels in Variable Methylated Loci using microarray data.
License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Suggests: 
    BiocStyle,
    knitr,
    rmarkdown,
    ggplot2,
    tidyr,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
Imports: 
    doRNG,
    dplyr,
    foreach,
    GenomicRanges,
    glmnet,
    IlluminaHumanMethylation450kanno.ilmn12.hg19,
    IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
    IlluminaHumanMethylationEPICv2anno.20a1.hg38,
    IRanges,
    iterators,
    lifecycle,
    magrittr,
    relaimpo,
    S4Vectors,
    stats,
    stringr,
    tibble
VignetteBuilder: knitr
Depends: 
    R (>= 4.2.0)
LazyData: true
URL: https://ericknavarrod.github.io/RAMEN/
BugReports: https://github.com/ErickNavarroD/RAMEN/issues

Scope

• Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):

  • data retrieval
  • data extraction
  • data munging
  • data deposition
  • data validation and testing
  • workflow automation
  • version control
  • citation management and bibliometrics
  • scientific software wrappers
  • field and lab reproducibility tools
  • database software bindings
  • geospatial data
  • translation

• Explain how and why the package falls under these categories (briefly, 1-2 sentences):
  The objective of the package is to provide a FAIR framework to analyze DNA methylation microarray, genotype and exposome data, and conduct a series of operations to model the association between DNA methylation and both genetic and environmental data. The RAMEN package puts together functions from different already-developed statistical packages to conduct the modelling, and is designed to conduct a specific analysis within the field of epigenetics.

• Who is the target audience and what are scientific applications of this package?
  The target audience of this package is researchers in the epigenetics field that have access to epidemiological cohorts with genetic, environmental and DNA methylation data. The main application of this package is to model the individual, additive and interactive contributions of genetics and environmental differences to genome-wide DNA methylation levels in a population.

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?
  To my knowledge there are no other R packages that accomplish the same thing.

• (If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?
  Yes.

• If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.
  This package is within the scope of rOpenSci, as the process of submitting RAMEN to peer review is my project for the rOpenSci Champions 2025 program.

• Explain reasons for any pkgcheck items which your package is unable to pass.

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Confirm each of the following by checking the box.

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• I have read the author guide and I expect to maintain this package for at least 2 years or to find a replacement.

This package:

• does not violate the Terms of Service of any service it interacts with.
• has a CRAN and OSI accepted license.
• contains a README with instructions for installing the development version.
• includes documentation with examples for all functions, created with roxygen2.
• contains a vignette with examples of its essential functions and uses.
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