{
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  "Title": "Exposure-Aware Multi-Omics Risk Modeling",
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  "Authors@R": "c(\nperson(\"Prem Prashant\", \"Chaudhary\",\nemail = \"chaudharyp2@nih.gov\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-3467-8608\"))\n)",
  "Description": "ExpoRiskR provides tools for exposure-aware multi-omics\nrisk modeling in translational and environmental health\nstudies. The package aligns sample identifiers across exposure\nand multi-omics blocks, performs lightweight preprocessing, and\nfits exposure-adjusted association models to build\ninterpretable microbe–metabolite networks. It also computes\nsimple exposure perturbation summaries and generates\npublication-ready visualizations. Workflows support both\nmatrix-based inputs and SummarizedExperiment objects.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
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  "URL": "https://github.com/ppchaudhary/ExpoRiskR",
  "BugReports": "https://github.com/ppchaudhary/ExpoRiskR/issues",
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  "biocViews": "Software, Network, SystemsBiology, Metabolomics, Microbiome,\nRegression",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:06:43 UTC",
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  "Author": "Prem Prashant Chaudhary [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-3467-8608>)",
  "Maintainer": "Prem Prashant Chaudhary <chaudharyp2@nih.gov>",
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      "page": "align_omics",
      "title": "Align exposures and multi-omics blocks by sample ID",
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      ]
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        "build_exposure_network"
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      ]
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        "generate_dummy_exporisk"
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      "page": "plot_exposure_network",
      "title": "Plot exposure-adjusted multi-omics network (bipartite)",
      "topics": [
        "plot_exposure_network"
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    },
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