Package: tidyexposomics 1.1.0

Jason Laird

tidyexposomics: Integrated Exposure-Omics Analysis Powered by Tidy Principles

The tidyexposomics package is designed to facilitate the integration of exposure and omics data to identify exposure-omics associations. We structure our commands to fit into the tidyverse framework, where commands are designed to be simplified and intuitive. Here we provide functionality to perform quality control, sample and exposure association analysis, differential abundance analysis, multi-omics integration, and functional enrichment analysis.

Authors:Jason Laird [aut, cre], Thomas Hartung [ctb], Fenna Sillé [ctb], Alexandra Maertens [ctb], JHU Discovery Award [fnd]

tidyexposomics_1.1.0.tar.gz
tidyexposomics_1.1.0.zip(r-4.7)tidyexposomics_1.1.0.zip(r-4.6)tidyexposomics_1.1.0.zip(r-4.5)
tidyexposomics_1.1.0.tgz(r-4.6-any)tidyexposomics_1.1.0.tgz(r-4.5-any)
tidyexposomics_1.1.0.tar.gz(r-4.7-any)tidyexposomics_1.1.0.tar.gz(r-4.6-any)
tidyexposomics_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
tidyexposomics/json (API)
NEWS

# Install 'tidyexposomics' in R:
install.packages('tidyexposomics', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bionomad/tidyexposomics/issues

Pkgdown/docs site:https://bionomad.github.io

Datasets:

On BioConductor:tidyexposomics-1.1.0(bioc 3.24)tidyexposomics-1.0.0(bioc 3.23)

softwaretranscriptomicsgeneexpressionepigeneticsproteomicsdifferentialexpressiondifferentialmethylationqualitycontrolgraphandnetworkmultiplecomparisonregressionstatisticalmethodvisualizationworkflowstep

5.72 score 1 stars 12 scripts 181 downloads 52 exports 228 dependencies

Last updated from:7d197e3038. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE329
linux-devel-x86_64OK708
source / vignettesOK497
linux-release-x86_64OK680
macos-release-arm64OK382
macos-oldrel-arm64OK384
windows-develOK511
windows-releaseOK481
windows-oldrelOK489
wasm-releaseOK291

Exports:build_ont_annot_appcreate_exposomicsetdownload_datasetextract_omics_exposure_dfextract_resultsextract_results_excelextract_top_factor_featuresfilter_missingfilter_non_normalfilter_omicsfilter_sample_outliersload_annotation_datamake_example_datapivot_exppivot_featurepivot_sampleplot_associationplot_circos_correlationplot_correlation_summaryplot_correlation_tileplot_enrichmentplot_exposure_impactplot_exposure_omics_associationplot_exposuresplot_factor_summaryplot_manhattanplot_missingplot_networkplot_normality_summaryplot_pcaplot_sample_clustersplot_sensitivity_summaryplot_top_factor_featuresplot_volcanorun_associationrun_cluster_samplesrun_correlationrun_create_networkrun_differential_abundancerun_enrichmentrun_exposome_scorerun_exposure_impactrun_exposure_omics_associationrun_factor_overlaprun_impute_missingrun_multiomics_integrationrun_normality_checkrun_pcarun_pipeline_summaryrun_sensitivity_analysisrun_summarize_exposurestransform_exposure

Dependencies:abindaskpassassertthatbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocParallelbitbit64blobbootbroombslibcachemcarcarDatacaretcheckmateclassclicliprclockclustercodetoolscolorspacecommonmarkcorpcorcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydendextendDerivdiagramdigestdoBydplyrDTe1071ellipseemmeansestimabilityevaluatefactoextraFactoMineRfarverfastmapfenrfilelockflashClustfontawesomeforcatsforeachforecastforeignformatRFormulafracdifffsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomicRangesggplot2ggpubrggrepelggsciggsignifglobalsgluegowergridExtragtablehardhathighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrhttr2igraphipredIRangesisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelavalazyevalleapslifecyclelimmalistenvlme4lmtestlubridatemagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamixOmicsModelMetricsmodelrmultcompViewMultiAssayExperimentmvtnormnaniarnlmenloptrnnetnormnumDerivopensslotelparallellypbapplypbkrtestpillarpkgconfigplotlyplyrpolynomprettyunitspROCprodlimprogressprogressrpromisesproxypurrrquantregR6rappdirsrARPACKrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrrecipesreformulasreshape2RGCCArglrlangrmarkdownrpartRSpectraRSQLiterstatixrstudioapirvestS4ArraysS4VectorsS7sassscalesscatterplot3dselectrSeqinfoshapeshinysnowsourcetoolsSparseArraySparseMsparsevctrsSQUAREMstatmodstringistringrSummarizedExperimentsurvivalsystibbletidybulktidyrtidyselecttimechangetimeDatetinytexttservicetzdbUpSetRurcautf8vctrsviridisviridisLitevisdatvroomwithrxfunxml2xtableXVectoryamlzoo

Custom Analysis

Jason Laird

Rendered fromcustom_analysis.Rmdusingknitr::rmarkdownon May 16 2026.

Last update: 2026-04-21
Started: 2026-04-21

Exposure Annotation

Jason Laird

Rendered fromexposure_annotation.Rmdusingknitr::rmarkdownon May 16 2026.

Last update: 2026-04-21
Started: 2026-04-21

Exposome Scores

Jason Laird

Rendered fromexposome_scores.Rmdusingknitr::rmarkdownon May 16 2026.

Last update: 2026-04-21
Started: 2026-04-21

Introduction to tidyexposomics

Jason Laird

Rendered fromtidyexposomics.Rmdusingknitr::rmarkdownon May 16 2026.

Last update: 2026-04-21
Started: 2025-03-30

Readme and manuals

Help Manual

Help pageTopics
Build the Ontology Annotation Shiny appbuild_ont_annot_app
Create an Exposomicset Objectcreate_exposomicset
Download and cache a tidyexposomics datasetdownload_dataset
Extract Merged Omics and Exposure Data Frameextract_omics_exposure_df
Extract Results from 'MultiAssayExperiment' Metadataextract_results
Export tidyexposomics Results to Excelextract_results_excel
Extract Top Contributing Features for Factorsextract_top_factor_features
Filter Features and Variables with High Missingnessfilter_missing
Filter Non-Normal Exposure Variablesfilter_non_normal
Filter low-quality features in omics assaysfilter_omics
Filter Sample Outliersfilter_sample_outliers
Load Ontology Dataload_annotation_data
Generate Example Data for Testingmake_example_data
Pivot a selected omics dataset from a MultiAssayExperiment into tidybulk formatpivot_exp
Extract Feature Metadata from a MultiAssayExperimentpivot_feature
Extract Sample Metadata from MultiAssayExperiment or SummarizedExperimentpivot_sample
Plot Association Results (Unified Forest Plot)plot_association
Plot Circular Network of Exposure Relationshipsplot_circos_correlation
Plot Correlation Summary from Exposure-Feature Correlationsplot_correlation_summary
Plot Correlation Tilemapplot_correlation_tile
Plot Enrichment Results from exposomicsetplot_enrichment
Plot Exposure Impact on Network Centrality Metricsplot_exposure_impact
Plot Exposure-Omics Associationsplot_exposure_omics_association
Plot Exposure Distributions by Category or Groupplot_exposures
Plot Summary of Factor Contributions from Multi-Omics Integrationplot_factor_summary
Plot a Manhattan-style ExWAS summary across omics categoriesplot_manhattan
Plot Missing Data Across Exposure and Omic Layersplot_missing
Plot Network Graph of Features or Exposuresplot_network
Plot Normality Summary of Exposure Variablesplot_normality_summary
Plot PCA Results for Features and Samplesplot_pca
Plot Sample Clustersplot_sample_clusters
Plot Sensitivity Analysis Summaryplot_sensitivity_summary
Plot Top Features by Factor from Integration Resultsplot_top_factor_features
Volcano Plot of Differential Abundanceplot_volcano
Run Association Analysisrun_association
Cluster Samples Based on Exposure Datarun_cluster_samples
Run Correlation Analysisrun_correlation
Create Correlation Network from Feature Datarun_create_network
Run Differential Abundance Analysisrun_differential_abundance
Perform enrichment analysis on selected features from a exposomicset objectrun_enrichment
Compute Composite Exposome Scoresrun_exposome_score
Calculate Exposure Impact from Feature-Exposure Correlation Networksrun_exposure_impact
Run Exposure-Omics Associationrun_exposure_omics_association
Identify and Annotate Shared Top Features Across Integration Factorsrun_factor_overlap
Impute Missing Exposure and Omics Data in a MultiAssayExperimentrun_impute_missing
Run Multi-Omics Integrationrun_multiomics_integration
Assess Normality of Exposure Variablesrun_normality_check
Perform Principal Component Analysis (PCA)run_pca
Summarize and Visualize Analysis Pipeline Stepsrun_pipeline_summary
Run Sensitivity Analysis for Differential Abundancerun_sensitivity_analysis
Summarize Exposure Variablesrun_summarize_exposures
Example exposome multi-omics datasettidyexposomics_example
Transform Exposure Variables for Normalitytransform_exposure