{
  "_id": "6ae9ce509ceaa78f2009d83d",
  "Package": "tidyexposomics",
  "Title": "Integrated Exposure-Omics Analysis Powered by Tidy Principles",
  "Version": "1.1.3",
  "Authors@R": "c(\nperson(given = \"Jason\",\nfamily  = \"Laird\",\nemail = \"jasonlaird5353@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0000-5994-2236\")\n),\nperson(given = \"Thomas\",\nfamily  = \"Hartung\",\nemail = \"thartun1@jhu.edu\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0003-1359-7689\")\n),\nperson(given = \"Fenna\",\nfamily  = \"Sillé\",\nemail = \"fsille1@jhu.edu\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0003-4305-2049\")\n),\nperson(given = \"Alexandra\",\nfamily  = \"Maertens\",\nemail = \"amaerte1@jhu.edu\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-2077-2011\")\n),\nperson(\"JHU Discovery Award\", role = \"fnd\")\n)",
  "Description": "The tidyexposomics package is designed to facilitate the\nintegration of exposure and omics data to identify\nexposure-omics associations. We structure our commands to fit\ninto the tidyverse framework, where commands are designed to be\nsimplified and intuitive. Here we provide functionality to\nperform quality control, sample and exposure association\nanalysis, differential abundance analysis, multi-omics\nintegration, and functional enrichment analysis.",
  "License": "MIT + file LICENSE",
  "URL": "https://bionomad.github.io/tidyexposomics/",
  "BugReports": "https://github.com/BioNomad/tidyexposomics/issues",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, Transcriptomics, GeneExpression, Epigenetics,\nProteomics, DifferentialExpression, DifferentialMethylation,\nQualityControl, GraphAndNetwork, MultipleComparison,\nRegression, StatisticalMethod, Visualization, WorkflowStep",
  "Config/testthat/edition": "3",
  "Config/roxygen2/version": "8.1.0",
  "Config/pak/sysreqs": "cmake libfreetype6-dev libglpk-dev make libicu-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev libx11-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-11-02 23:06:45 UTC",
  "RemoteUrl": "https://github.com/bioc/tidyexposomics",
  "RemoteRef": "HEAD",
  "RemoteSha": "d279dc76136ae166e12fc440e82ff8620a435e80",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-11-03 10:01:46 UTC",
    "User": "root"
  },
  "Author": "Jason Laird [aut, cre] (ORCID: <https://orcid.org/0009-0000-5994-2236>),\nThomas Hartung [ctb] (ORCID: <https://orcid.org/0000-0003-1359-7689>),\nFenna Sillé [ctb] (ORCID: <https://orcid.org/0000-0003-4305-2049>),\nAlexandra Maertens [ctb] (ORCID:\n<https://orcid.org/0000-0002-2077-2011>),\nJHU Discovery Award [fnd]",
  "Maintainer": "Jason Laird <jasonlaird5353@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "tidyexposomics_1.1.3.tar.gz",
  "_fileid": "https://r2.ropensci.org/a0250e70685d22dcaccacbfe717498f326316fa9774f6b9c0da3b604683aa10f",
  "_filesize": 6973305,
  "_sha256": "a0250e70685d22dcaccacbfe717498f326316fa9774f6b9c0da3b604683aa10f",
  "_expires": "2027-02-11T12:06:38.000Z",
  "_created": "2026-11-03T10:01:46.000Z",
  "_published": "2026-11-03T12:06:40.775Z",
  "_upstream": "https://github.com/bioc/tidyexposomics",
  "_status": "success",
  "_maintainer": {
    "name": "Jason Laird",
    "email": "jasonlaird5353@gmail.com",
    "login": "bionomad",
    "description": "Computational biologist and toxicologist working to advance research topics in neurology and immunology.",
    "uuid": 59677194,
    "orcid": "0009-0000-5994-2236"
  },
  "_jobs": [
    {
      "job": 125849262087,
      "time": 249,
      "config": "bioc-checks",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13221572089"
    },
    {
      "job": 125849261871,
      "time": 567,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "13221104614"
    },
    {
      "job": 125849261824,
      "time": 586,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13221871439"
    },
    {
      "job": 125849261853,
      "time": 464,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "13229071101"
    },
    {
      "job": 125849261896,
      "time": 427,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13228848515"
    },
    {
      "job": 125845512175,
      "time": 446,
      "config": "source",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13220474787"
    },
    {
      "job": 125849261841,
      "time": 232,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13221691688"
    },
    {
      "job": 125849261873,
      "time": 426,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "13221980879"
    },
    {
      "job": 125849261909,
      "time": 461,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "13221123343"
    },
    {
      "job": 125849261921,
      "time": 423,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13222031299"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41614693562",
  "_commit": {
    "id": "d279dc76136ae166e12fc440e82ff8620a435e80",
    "author": "BioNomad <jlaird1@binghamton.edu>",
    "committer": "BioNomad <jlaird1@binghamton.edu>",
    "message": "1.1.3 updates\n",
    "time": 1793660805
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "MultiAssayExperiment",
      "role": "Depends"
    },
    {
      "package": "BiocFileCache",
      "role": "Imports"
    },
    {
      "package": "broom",
      "role": "Imports"
    },
    {
      "package": "cluster",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "DT",
      "role": "Imports"
    },
    {
      "package": "factoextra",
      "role": "Imports"
    },
    {
      "package": "fenr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.4.0",
      "role": "Imports"
    },
    {
      "package": "ggpubr",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "Hmisc",
      "role": "Imports"
    },
    {
      "package": "httr",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "naniar",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidybulk",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "circlize",
      "role": "Suggests"
    },
    {
      "package": "curl",
      "role": "Suggests"
    },
    {
      "package": "densityClust",
      "role": "Suggests"
    },
    {
      "package": "DiagrammeR",
      "role": "Suggests"
    },
    {
      "package": "dynamicTreeCut",
      "role": "Suggests"
    },
    {
      "package": "edgeR",
      "role": "Suggests"
    },
    {
      "package": "forcats",
      "role": "Suggests"
    },
    {
      "package": "ggh4x",
      "role": "Suggests"
    },
    {
      "package": "ggnewscale",
      "role": "Suggests"
    },
    {
      "package": "ggraph",
      "role": "Suggests"
    },
    {
      "package": "ggridges",
      "role": "Suggests"
    },
    {
      "package": "ggsci",
      "role": "Suggests"
    },
    {
      "package": "ggvenn",
      "role": "Suggests"
    },
    {
      "package": "grid",
      "role": "Suggests"
    },
    {
      "package": "gridExtra",
      "role": "Suggests"
    },
    {
      "package": "impute",
      "role": "Suggests"
    },
    {
      "package": "janitor",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "matrixStats",
      "role": "Suggests"
    },
    {
      "package": "mice",
      "role": "Suggests"
    },
    {
      "package": "mirt",
      "role": "Suggests"
    },
    {
      "package": "missForest",
      "role": "Suggests"
    },
    {
      "package": "mixOmics",
      "role": "Suggests"
    },
    {
      "package": "MOFA2",
      "role": "Suggests"
    },
    {
      "package": "nipalsMCIA",
      "role": "Suggests"
    },
    {
      "package": "openxlsx",
      "role": "Suggests"
    },
    {
      "package": "patchwork",
      "role": "Suggests"
    },
    {
      "package": "reticulate",
      "role": "Suggests"
    },
    {
      "package": "RGCCA",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "Seurat",
      "role": "Suggests"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "tidygraph",
      "role": "Suggests"
    },
    {
      "package": "tidyHeatmap",
      "role": "Suggests"
    },
    {
      "package": "tidyselect",
      "role": "Suggests"
    },
    {
      "package": "tidytext",
      "role": "Suggests"
    },
    {
      "package": "tidyverse",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-49",
      "n": 1
    },
    {
      "week": "2025-51",
      "n": 1
    },
    {
      "week": "2026-02",
      "n": 2
    },
    {
      "week": "2026-11",
      "n": 1
    },
    {
      "week": "2026-15",
      "n": 1
    },
    {
      "week": "2026-16",
      "n": 2
    },
    {
      "week": "2026-17",
      "n": 1
    },
    {
      "week": "2026-27",
      "n": 3
    },
    {
      "week": "2026-32",
      "n": 1
    },
    {
      "week": "2026-45",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.1.2",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.0.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "software",
    "transcriptomics",
    "geneexpression",
    "epigenetics",
    "proteomics",
    "differentialexpression",
    "differentialmethylation",
    "qualitycontrol",
    "graphandnetwork",
    "multiplecomparison",
    "regression",
    "statisticalmethod",
    "visualization",
    "workflowstep"
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "bionomad",
      "count": 138,
      "uuid": 59677194
    },
    {
      "user": "jwokaty",
      "count": 2,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 484,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 222,
    "source": "https://www.bioconductor.org/packages/stats/bioc/tidyexposomics"
  },
  "_devurl": "https://github.com/bionomad/tidyexposomics",
  "_pkgdown": "https://bionomad.github.io/tidyexposomics/",
  "_searchresults": 29,
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/tidyexposomics.html",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/bionomad/tidyexposomics",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "association_models",
    "build_ont_annot_app",
    "compare_association",
    "create_exposomicset",
    "download_dataset",
    "extract_omics_exposure_df",
    "extract_results",
    "extract_results_excel",
    "extract_top_factor_features",
    "filter_missing",
    "filter_non_normal",
    "filter_omics",
    "filter_sample_outliers",
    "load_annotation_data",
    "make_example_data",
    "make_example_sc",
    "make_example_sce_codebook",
    "pivot_exp",
    "pivot_feature",
    "pivot_sample",
    "plot_association",
    "plot_association_comparison",
    "plot_circos_correlation",
    "plot_clusters",
    "plot_correlation_summary",
    "plot_correlation_tile",
    "plot_enrichment",
    "plot_exposure_impact",
    "plot_exposure_omics_association",
    "plot_exposures",
    "plot_factor_summary",
    "plot_manhattan",
    "plot_missing",
    "plot_network",
    "plot_normality_summary",
    "plot_pca",
    "plot_sample_clusters",
    "plot_sensitivity_summary",
    "plot_top_factor_features",
    "plot_volcano",
    "run_association",
    "run_cluster_exposures",
    "run_cluster_samples",
    "run_correlation",
    "run_create_network",
    "run_differential_abundance",
    "run_enrichment",
    "run_exposome_score",
    "run_exposure_impact",
    "run_exposure_omics_association",
    "run_factor_overlap",
    "run_impute_missing",
    "run_multiomics_integration",
    "run_normality_check",
    "run_pca",
    "run_pipeline_summary",
    "run_sensitivity_analysis",
    "run_summarize_exposures",
    "transform_exposure",
    "transform_sce_to_exposomicset"
  ],
  "_datasets": [
    {
      "name": "tidyexposomics_example",
      "title": "Example exposome multi-omics dataset",
      "object": "tidyexposomics_example",
      "file": "tidyexposomics_example.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "association_models",
      "title": "List Stored Association Models",
      "topics": [
        "association_models"
      ]
    },
    {
      "page": "build_ont_annot_app",
      "title": "Build the Ontology Annotation Shiny app",
      "topics": [
        "build_ont_annot_app"
      ]
    },
    {
      "page": "compare_association",
      "title": "Compare Association Models",
      "topics": [
        "compare_association"
      ]
    },
    {
      "page": "create_exposomicset",
      "title": "Create an Exposomicset Object",
      "topics": [
        "create_exposomicset"
      ]
    },
    {
      "page": "download_dataset",
      "title": "Download and cache a tidyexposomics dataset",
      "topics": [
        "download_dataset"
      ]
    },
    {
      "page": "extract_omics_exposure_df",
      "title": "Extract Merged Omics and Exposure Data Frame",
      "topics": [
        "extract_omics_exposure_df"
      ]
    },
    {
      "page": "extract_results",
      "title": "Extract Results from 'MultiAssayExperiment' Metadata",
      "topics": [
        "extract_results"
      ]
    },
    {
      "page": "extract_results_excel",
      "title": "Export tidyexposomics Results to Excel",
      "topics": [
        "extract_results_excel"
      ]
    },
    {
      "page": "extract_top_factor_features",
      "title": "Extract Top Contributing Features for Factors",
      "topics": [
        "extract_top_factor_features"
      ]
    },
    {
      "page": "filter_missing",
      "title": "Filter Features and Variables with High Missingness",
      "topics": [
        "filter_missing"
      ]
    },
    {
      "page": "filter_non_normal",
      "title": "Filter Non-Normal Exposure Variables",
      "topics": [
        "filter_non_normal"
      ]
    },
    {
      "page": "filter_omics",
      "title": "Filter low-quality features in omics assays",
      "topics": [
        "filter_omics"
      ]
    },
    {
      "page": "filter_sample_outliers",
      "title": "Filter Sample Outliers",
      "topics": [
        "filter_sample_outliers"
      ]
    },
    {
      "page": "load_annotation_data",
      "title": "Load Ontology Data",
      "topics": [
        "load_annotation_data"
      ]
    },
    {
      "page": "make_example_data",
      "title": "Generate Example Data for Testing",
      "topics": [
        "make_example_data"
      ]
    },
    {
      "page": "make_example_sc",
      "title": "Make an example single-cell dataset with multiple exposures",
      "topics": [
        "make_example_sc"
      ]
    },
    {
      "page": "make_example_sce_codebook",
      "title": "Make an example codebook for the simulated single-cell data",
      "topics": [
        "make_example_sce_codebook"
      ]
    },
    {
      "page": "pivot_exp",
      "title": "Pivot a selected omics dataset from a MultiAssayExperiment into tidybulk format",
      "topics": [
        "pivot_exp"
      ]
    },
    {
      "page": "pivot_feature",
      "title": "Extract Feature Metadata from a MultiAssayExperiment",
      "topics": [
        "pivot_feature"
      ]
    },
    {
      "page": "pivot_sample",
      "title": "Extract Sample Metadata from MultiAssayExperiment or SummarizedExperiment",
      "topics": [
        "pivot_sample"
      ]
    },
    {
      "page": "plot_association",
      "title": "Plot Association Results",
      "topics": [
        "plot_association"
      ]
    },
    {
      "page": "plot_association_comparison",
      "title": "Plot an Association Model Comparison",
      "topics": [
        "plot_association_comparison"
      ]
    },
    {
      "page": "plot_circos_correlation",
      "title": "Plot Circular Network of Exposure Relationships",
      "topics": [
        "plot_circos_correlation"
      ]
    },
    {
      "page": "plot_clusters",
      "title": "Plot Sample or Exposure Clusters",
      "topics": [
        "plot_clusters"
      ]
    },
    {
      "page": "plot_correlation_summary",
      "title": "Plot Correlation Summary from Exposure-Feature Correlations",
      "topics": [
        "plot_correlation_summary"
      ]
    },
    {
      "page": "plot_correlation_tile",
      "title": "Plot Correlation Tilemap",
      "topics": [
        "plot_correlation_tile"
      ]
    },
    {
      "page": "plot_enrichment",
      "title": "Plot Enrichment Results from exposomicset",
      "topics": [
        "plot_enrichment"
      ]
    },
    {
      "page": "plot_exposure_impact",
      "title": "Plot Exposure Impact on Network Centrality Metrics",
      "topics": [
        "plot_exposure_impact"
      ]
    },
    {
      "page": "plot_exposure_omics_association",
      "title": "Plot Exposure-Omics Associations",
      "topics": [
        "plot_exposure_omics_association"
      ]
    },
    {
      "page": "plot_exposures",
      "title": "Plot Exposure Distributions by Category or Group",
      "topics": [
        "plot_exposures"
      ]
    },
    {
      "page": "plot_factor_summary",
      "title": "Plot Summary of Factor Contributions from Multi-Omics Integration",
      "topics": [
        "plot_factor_summary"
      ]
    },
    {
      "page": "plot_manhattan",
      "title": "Plot a Manhattan-style ExWAS summary across omics categories",
      "topics": [
        "plot_manhattan"
      ]
    },
    {
      "page": "plot_missing",
      "title": "Plot Missing Data Across Exposure and Omic Layers",
      "topics": [
        "plot_missing"
      ]
    },
    {
      "page": "plot_network",
      "title": "Plot Network Graph of Features or Exposures",
      "topics": [
        "plot_network"
      ]
    },
    {
      "page": "plot_normality_summary",
      "title": "Plot Normality Summary of Exposure Variables",
      "topics": [
        "plot_normality_summary"
      ]
    },
    {
      "page": "plot_pca",
      "title": "Plot PCA Results for Features and Samples",
      "topics": [
        "plot_pca"
      ]
    },
    {
      "page": "plot_sample_clusters",
      "title": "Plot Sample Clusters",
      "topics": [
        "plot_sample_clusters"
      ]
    },
    {
      "page": "plot_sensitivity_summary",
      "title": "Plot Sensitivity Analysis Summary",
      "topics": [
        "plot_sensitivity_summary"
      ]
    },
    {
      "page": "plot_top_factor_features",
      "title": "Plot Top Features by Factor from Integration Results",
      "topics": [
        "plot_top_factor_features"
      ]
    },
    {
      "page": "plot_volcano",
      "title": "Volcano Plot of Differential Abundance",
      "topics": [
        "plot_volcano"
      ]
    },
    {
      "page": "run_association",
      "title": "Run Association Analysis",
      "topics": [
        "run_association"
      ]
    },
    {
      "page": "run_cluster_exposures",
      "title": "Cluster Exposures Based on Scaled Exposure Data",
      "topics": [
        "run_cluster_exposures"
      ]
    },
    {
      "page": "run_cluster_samples",
      "title": "Cluster Samples Based on Exposure Data",
      "topics": [
        "run_cluster_samples"
      ]
    },
    {
      "page": "run_correlation",
      "title": "Run Correlation Analysis",
      "topics": [
        "run_correlation"
      ]
    },
    {
      "page": "run_create_network",
      "title": "Create Correlation Network from Feature Data",
      "topics": [
        "run_create_network"
      ]
    },
    {
      "page": "run_differential_abundance",
      "title": "Run Differential Abundance Analysis",
      "topics": [
        "run_differential_abundance"
      ]
    },
    {
      "page": "run_enrichment",
      "title": "Run functional enrichment on omics features",
      "topics": [
        "run_enrichment"
      ]
    },
    {
      "page": "run_exposome_score",
      "title": "Compute Composite Exposome Scores",
      "topics": [
        "run_exposome_score"
      ]
    },
    {
      "page": "run_exposure_impact",
      "title": "Calculate Exposure Impact from Feature-Exposure Correlation Networks",
      "topics": [
        "run_exposure_impact"
      ]
    },
    {
      "page": "run_exposure_omics_association",
      "title": "Run Exposure-Omics Association",
      "topics": [
        "run_exposure_omics_association"
      ]
    },
    {
      "page": "run_factor_overlap",
      "title": "Identify and Annotate Shared Top Features Across Integration Factors",
      "topics": [
        "run_factor_overlap"
      ]
    },
    {
      "page": "run_impute_missing",
      "title": "Impute Missing Exposure and Omics Data in a MultiAssayExperiment",
      "topics": [
        "run_impute_missing"
      ]
    },
    {
      "page": "run_multiomics_integration",
      "title": "Run Multi-Omics Integration",
      "topics": [
        "run_multiomics_integration"
      ]
    },
    {
      "page": "run_normality_check",
      "title": "Assess Normality of Exposure Variables",
      "topics": [
        "run_normality_check"
      ]
    },
    {
      "page": "run_pca",
      "title": "Perform Principal Component Analysis (PCA)",
      "topics": [
        "run_pca"
      ]
    },
    {
      "page": "run_pipeline_summary",
      "title": "Summarize and Visualize Analysis Pipeline Steps",
      "topics": [
        "run_pipeline_summary"
      ]
    },
    {
      "page": "run_sensitivity_analysis",
      "title": "Run Sensitivity Analysis for Differential Abundance",
      "topics": [
        "run_sensitivity_analysis"
      ]
    },
    {
      "page": "run_summarize_exposures",
      "title": "Summarize Exposure Variables",
      "topics": [
        "run_summarize_exposures"
      ]
    },
    {
      "page": "tidyexposomics_example",
      "title": "Example exposome multi-omics dataset",
      "topics": [
        "tidyexposomics_example"
      ]
    },
    {
      "page": "transform_exposure",
      "title": "Transform Exposure Variables for Normality",
      "topics": [
        "transform_exposure"
      ]
    },
    {
      "page": "transform_sce_to_exposomicset",
      "title": "Convert a SingleCellExperiment or Seurat Object to an exposomicset",
      "topics": [
        "transform_sce_to_exposomicset"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/tidyexposomics/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "assertthat",
    "backports",
    "base64enc",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "bit",
    "bit64",
    "blob",
    "boot",
    "broom",
    "bslib",
    "cachem",
    "car",
    "carData",
    "checkmate",
    "cli",
    "clipr",
    "cluster",
    "colorspace",
    "commonmark",
    "corrplot",
    "cowplot",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dendextend",
    "Deriv",
    "digest",
    "doBy",
    "dplyr",
    "DT",
    "ellipse",
    "emmeans",
    "estimability",
    "evaluate",
    "factoextra",
    "FactoMineR",
    "farver",
    "fastmap",
    "fenr",
    "filelock",
    "flashClust",
    "fontawesome",
    "forcats",
    "forecast",
    "foreign",
    "Formula",
    "fracdiff",
    "fs",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "ggpubr",
    "ggrepel",
    "ggsci",
    "ggsignif",
    "glue",
    "gridExtra",
    "gtable",
    "highr",
    "Hmisc",
    "hms",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "httr2",
    "igraph",
    "IRanges",
    "irlba",
    "isoband",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "leaps",
    "lifecycle",
    "limma",
    "lme4",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "memoise",
    "mgcv",
    "mime",
    "minqa",
    "modelr",
    "multcompView",
    "MultiAssayExperiment",
    "mvtnorm",
    "naniar",
    "nlme",
    "nloptr",
    "nnet",
    "norm",
    "numDeriv",
    "openssl",
    "otel",
    "pbkrtest",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "polynom",
    "prettyunits",
    "progress",
    "promises",
    "purrr",
    "quantreg",
    "R6",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "readr",
    "reformulas",
    "rlang",
    "rmarkdown",
    "rpart",
    "RSQLite",
    "rstatix",
    "rstudioapi",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "scatterplot3d",
    "Seqinfo",
    "shiny",
    "showtext",
    "showtextdb",
    "sourcetools",
    "SparseArray",
    "SparseM",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "sysfonts",
    "tibble",
    "tidybulk",
    "tidyr",
    "tidyselect",
    "timeDate",
    "tinytex",
    "ttservice",
    "tzdb",
    "UpSetR",
    "urca",
    "utf8",
    "vctrs",
    "viridis",
    "viridisLite",
    "visdat",
    "vroom",
    "withr",
    "xfun",
    "xtable",
    "XVector",
    "yaml",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "exposure_omics_phenotype_workflow.Rmd",
      "filename": "exposure_omics_phenotype_workflow.html",
      "title": "Exposure-Omics-Phenotype Workflow",
      "author": "Jason Laird",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Exposure Preprocessing",
        "Getting the data in order",
        "Quality Control",
        "Missingness",
        "Imputation",
        "Normality Check",
        "Exposure Summary",
        "Exposure Visualization",
        "Coverting the Exposomicset back to dataframes",
        "ExWAS",
        "Exposome-wide association study (ExWAS)",
        "Interaction Modeling",
        "Stratifying Models",
        "Comparing models",
        "Omics Preprocessing",
        "Filtering Omics Features",
        "Differential Abundance",
        "Exposure-Omics Association",
        "Biological Interpretation",
        "Enrichment Analysis",
        "Enrichment Visualizations",
        "Enrichment Summary",
        "DotPlot",
        "Term Network Plot",
        "Heatmap",
        "Cnet Plot"
      ],
      "created": "2026-11-02 23:06:45",
      "modified": "2026-11-02 23:06:45",
      "commits": 1
    },
    {
      "source": "exposure_phenotype_workflow.Rmd",
      "filename": "exposure_phenotype_workflow.html",
      "title": "Exposure-Phenotype Workflow",
      "author": "Jason Laird",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Exposure Preprocessing",
        "Getting the data in order",
        "Quality Control",
        "Missingness",
        "Imputation",
        "Normality Check",
        "Exposure Summary",
        "Exposure Visualization",
        "Coverting the Exposomicset back to dataframes",
        "Exposure/Sample Clustering",
        "Co-exposure",
        "Exposure Correlations",
        "Exposure Clusters",
        "Sample Clustering",
        "ExWAS",
        "Exposome-wide association study (ExWAS)",
        "Interaction Modeling",
        "Stratifying Models",
        "Comparing models",
        "Exposome Scores"
      ],
      "created": "2026-11-02 23:06:45",
      "modified": "2026-11-02 23:06:45",
      "commits": 1
    },
    {
      "source": "tidyexposomics.Rmd",
      "filename": "tidyexposomics.html",
      "title": "Getting Started with tidyexposomics",
      "author": "Jason Laird",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Exposure-Phenotype Analysis",
        "Exposure-Phenotype-Omics Analysis"
      ],
      "created": "2025-03-30 19:47:15",
      "modified": "2026-11-02 23:06:45",
      "commits": 25
    }
  ],
  "_score": 5.939519252618618,
  "_indexed": true,
  "_nocasepkg": "tidyexposomics",
  "_universes": [
    "bioc",
    "bionomad"
  ],
  "_previous": "1.1.2",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.3",
      "date": "2026-11-03T10:07:10.000Z",
      "distro": "resolute",
      "commit": "d279dc76136ae166e12fc440e82ff8620a435e80",
      "fileid": "https://r2.ropensci.org/00366eb2ba26f8ed3fbe657b1eb1f418532890bbb35caf5b2ed0a9703021487d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41614693562"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.1.3",
      "date": "2026-11-03T10:07:55.000Z",
      "distro": "resolute",
      "commit": "d279dc76136ae166e12fc440e82ff8620a435e80",
      "fileid": "https://r2.ropensci.org/4afa4350f11ad953992c6d459104ba03eaf088af95537d4f5e26eabc4f40a5b6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41614693562"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.3",
      "date": "2026-11-03T11:59:53.000Z",
      "commit": "d279dc76136ae166e12fc440e82ff8620a435e80",
      "fileid": "https://r2.ropensci.org/f3466ddabcc6003a6bcdb668faa07c3f0a7a40981898728fd7acdbed3563a416",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41614693562"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.1.3",
      "date": "2026-11-03T12:01:29.000Z",
      "commit": "d279dc76136ae166e12fc440e82ff8620a435e80",
      "fileid": "https://r2.ropensci.org/df165272839938e85482d652d3cadfebbfc0a2b9793cafa1862740ac80d4a7b4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41614693562"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.3",
      "date": "2026-11-03T10:06:21.000Z",
      "commit": "d279dc76136ae166e12fc440e82ff8620a435e80",
      "fileid": "https://r2.ropensci.org/57dd2dad1542daa455d826d568b62bc7e899d7b002ac05bf27120a3d404c5a8d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41614693562"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.3",
      "date": "2026-11-03T10:04:14.000Z",
      "commit": "d279dc76136ae166e12fc440e82ff8620a435e80",
      "fileid": "https://r2.ropensci.org/ac54c47f7aaacf0216cbbb7bcdc982e3f189f3ab5637b34b0327eb6372950cd2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41614693562"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.3",
      "date": "2026-11-03T10:04:49.000Z",
      "commit": "d279dc76136ae166e12fc440e82ff8620a435e80",
      "fileid": "https://r2.ropensci.org/57a5761493235a88e5df8d4197a0e288e35a6562d00b2322861db71945ecfc88",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41614693562"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.1.3",
      "date": "2026-11-03T10:04:37.000Z",
      "commit": "d279dc76136ae166e12fc440e82ff8620a435e80",
      "fileid": "https://r2.ropensci.org/571a677d614cbc8f9364fc36736271f4beefaedc5f469bbcdc1f45dcdd3a77c6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41614693562"
    }
  ]
}