{
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  "Package": "CGEN",
  "Title": "An R package for analysis of case-control studies in genetic\nepidemiology",
  "Version": "3.49.0",
  "Date": "2012-10-10",
  "Authors@R": "c( \nperson(\"Samsiddhi\", \"Bhattacharjee\", role = c(\"aut\")),\nperson(\"Nilanjan\", \"Chatterjee\", role = c(\"aut\")),\nperson(\"Summer\", \"Han\", role = c(\"aut\")),\nperson(\"Minsun\", \"Song\", role = c(\"aut\")),\nperson(\"William\", \"Wheeler\", role = c(\"aut\")),\nperson(\"Matthieu\", \"de Rochemonteix\", role = c(\"aut\")),\nperson(\"Nilotpal\", \"Sanyal\", role = c(\"aut\")),\nperson(\"Justin\", \"Lee\", role = c(\"cre\"), email = \"jhylee@stanford.edu\")\n)",
  "Description": "This is a package for analysis of case-control data in\ngenetic epidemiology. It provides a set of statistical methods\nfor evaluating gene-environment (or gene-genes) interactions\nunder multiplicative and additive risk models, with or without\nassuming gene-environment (or gene-gene) independence in the\nunderlying population.",
  "License": "GPL-2 + file LICENSE",
  "biocViews": "SNP, MultipleComparison, Clustering",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:55:47 UTC",
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