{
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  "Package": "RAMEN",
  "Title": "Regional Association of Methylome variability with the Exposome\nand geNome",
  "Version": "2.99.0",
  "Authors@R": "c(\nperson(\"Erick I.\", \"Navarro-Delgado\",\nemail = \"erick.delgado@ubc.ca\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-1040-3519\")),\nperson(\"Keegan\", \"Korthauer\",\nrole = \"aut\",\nemail = \"keegan@stat.ubc.ca\",\ncomment = c(ORCID = \"0000-0002-4565-1654\")),\nperson(\"Michael S.\", \"Kobor\",\nemail = \"michael.kobor@ubc.ca\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0003-4140-1743\")),\nperson(\"Lluís\", \"Revilla Sancho\",\nemail = \"lluis.revilla@gmail.com\",\nrole = \"rev\",\ncomment = c(ORCID = \"0000-0001-9747-2570\")),\nperson(\"Ulduz\", \"Vafadarshamasbi\",\nemail = \"vafadar.u@uq.edu.au\",\nrole = \"rev\",\ncomment = c(ORCID = \"0000-0002-8370-8084\")),\nperson(\"The University of British Columbia\", role = \"fnd\")\n)",
  "Description": "RAMEN is an R package which goal is to identify Variable\nMethylated Loci (VML) in microarray DNA methylation data and\nthen, using genome and exposome data, identify which individual\ngenetic (G) or environmental (E) or joint (G+E or GxE) model\nbetter explains the VML variability. This package provides\nestimates of genetic and environmental contribution for each\nVML, allowing researchers to gain insights into the complex\ninterplay between genetics, environment and DNA methylation.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "biocViews": "DNAMethylation, GenomeWideAssociation, Epigenetics,\nRegression, SNP, Microarray, MethylationArray,\nGeneticVariability",
  "Roxygen": "list(markdown = TRUE)",
  "Config/testthat/edition": "3",
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  "URL": "https://ropensci.github.io/RAMEN/ ,\nhttps://github.com/ropensci/RAMEN/",
  "BugReports": "https://github.com/ropensci/RAMEN/issues",
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  "Repository": "https://ropensci.r-universe.dev",
  "Date/Publication": "2026-08-29 00:11:23 UTC",
  "RemoteUrl": "https://github.com/ropensci/RAMEN",
  "RemoteRef": "main",
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  "Packaged": {
    "Date": "2026-08-29 09:44:31 UTC",
    "User": "root"
  },
  "Author": "Erick I. Navarro-Delgado [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-1040-3519>),\nKeegan Korthauer [aut] (ORCID: <https://orcid.org/0000-0002-4565-1654>),\nMichael S. Kobor [aut] (ORCID: <https://orcid.org/0000-0003-4140-1743>),\nLluís Revilla Sancho [rev] (ORCID:\n<https://orcid.org/0000-0001-9747-2570>),\nUlduz Vafadarshamasbi [rev] (ORCID:\n<https://orcid.org/0000-0002-8370-8084>),\nThe University of British Columbia [fnd]",
  "Maintainer": "Erick I. Navarro-Delgado <erick.delgado@ubc.ca>",
  "_user": "ropensci",
  "_type": "src",
  "_file": "RAMEN_2.99.0.tar.gz",
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  "_expires": "2026-12-07T10:40:22.000Z",
  "_created": "2026-08-29T09:44:31.000Z",
  "_published": "2026-08-31T07:58:35.887Z",
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      "source": "RAMEN.Rmd",
      "filename": "RAMEN.html",
      "title": "RAMEN",
      "author": "Erick I. Navarro-Delgado",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Citation",
        "Gene-environment interaction analysis",
        "Data expectations",
        "RAMEN's underlying assumptions",
        "Genomic data",
        "DNA methylation data",
        "Exposome data",
        "Covariates to include",
        "Workflow overview",
        "Install RAMEN and set up environment",
        "Identify VML and summarize their methylation state",
        "Note on argument: var_method",
        "Note on argument: var_distribution",
        "Running RAMEN::findVML()",
        "Identify cis SNPs",
        "Conduct variable selection on genome and exposome variables",
        "Author's note about variables interpretation",
        "Identify the best explanatory model (G/E/G+E/GxE) per VML",
        "Fit and compare the models and select the best one",
        "Remove poor performing winning models",
        "Author's note about model interpretation",
        "Variations to the standard workflow",
        "Frequently Asked Questions",
        "How can I save the RAMEN data frames that have columns with lists as observations?",
        "How can I set up the parallel backend?",
        "Session info"
      ],
      "created": "2023-11-01 01:05:46",
      "modified": "2026-08-28 22:40:54",
      "commits": 18
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