Package: tidyexposomics 1.1.1

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_1.1.1.tar.gz
tidyexposomics_1.1.1.zip(r-4.7)tidyexposomics_1.1.1.zip(r-4.6)tidyexposomics_1.1.1.zip(r-4.5)
tidyexposomics_1.1.1.tgz(r-4.6-any)tidyexposomics_1.1.1.tgz(r-4.5-any)
tidyexposomics_1.1.1.tar.gz(r-4.7-any)tidyexposomics_1.1.1.tar.gz(r-4.6-any)
tidyexposomics_1.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
tidyexposomics/json (API)

# 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

5.64 score 1 stars 12 scripts 53 exports 237 dependencies

Last updated from:4725f84037. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE281
linux-devel-x86_64OK665
source / vignettesOK493
linux-release-x86_64OK661
macos-release-arm64OK397
macos-oldrel-arm64OK289
windows-develOK522
windows-releaseOK510
windows-oldrelOK448
wasm-releaseOK327

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_exposuretransform_sce_to_exposomicset

Dependencies:abindaskpassassertthatbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocParallelbitbit64blobbootbroombslibcachemcarcarDatacaretcheckmateclassclicliprclockclustercodetoolscolorspacecommonmarkcorpcorcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydendextendDerivdiagramdigestdoBydplyrDTe1071ellipseemmeansestimabilityevaluatefactoextraFactoMineRfarverfastmapfenrfilelockflashClustfontawesomeforcatsforeachforecastforeignformatRFormulafracdifffsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomicRangesggplot2ggpubrggrepelggsciggsignifggtextglobalsgluegowergridExtragridtextgtablehardhathighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrhttr2igraphipredIRangesirlbaisobanditeratorsjpegjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelavalazyevalleapslifecyclelimmalistenvlitedownlme4lmtestlubridatemagrittrmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmimeminqamixOmicsModelMetricsmodelrmultcompViewMultiAssayExperimentmvtnormnaniarnlmenloptrnnetnormnumDerivopensslotelparallellypbapplypbkrtestpillarpkgconfigplotlyplyrpngpolynomprettyunitspROCprodlimprogressprogressrpromisesproxypurrrquantregR6rappdirsrARPACKrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrrecipesreformulasreshape2RGCCArglrlangrmarkdownrpartRSpectraRSQLiterstatixrstudioapirvestS4ArraysS4VectorsS7sassscalesscatterplot3dselectrSeqinfoshapeshinyshowtextshowtextdbsnowsourcetoolsSparseArraySparseMsparsevctrsSQUAREMstatmodstringistringrSummarizedExperimentsurvivalsyssysfontstibbletidybulktidyrtidyselecttimechangetimeDatetinytexttservicetzdbUpSetRurcautf8vctrsviridisviridisLitevisdatvroomwithrxfunxml2xtableXVectoryamlzoo

Custom Analysis
Load Data and Libraries | Pivot Sample | Pivot Feature | Pivot Experiment | Session Info
Rendered fromcustom_analysis.Rmdusingknitr::rmarkdown

Last update: 2026-07-04
Started: 2026-04-21

Exposure Annotation
Exposure Metadata and Ontology Annotation | Codebook Setup | Ontology Choices | Ontology Annotation App | Session Info
Rendered fromexposure_annotation.Rmdusingknitr::rmarkdown

Last update: 2026-07-04
Started: 2026-04-21

Exposome Scores
Load Data and Libraries | Quality Control | Session Info
Rendered fromexposome_scores.Rmdusingknitr::rmarkdown

Last update: 2026-07-04
Started: 2026-04-21

Introduction to tidyexposomics
Installation | Command Structure | Quality Control | Missingness | Plot missing variables withing exposure group | Filtering Omics Features | Normality Check | Principal Component Analysis | Plot the correlation tile plot | Exposure Visualization | Sample-Exposure Association | Sample Clustering | Exposure Correlations | Exposure-wide association (ExWAS) | Differential Abundance | Exposure-Omics Association | Enrichment Analysis | Enrichment Visualizations | Enrichment Summary | DotPlot | Term Network Plot | Heatmap | Cnet Plot | Pipeline Summary | Saving Results | Session Info | References
Rendered fromtidyexposomics.Rmdusingknitr::rmarkdown

Last update: 2026-07-04
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
Convert a SingleCellExperiment to an exposomicsettransform_sce_to_exposomicset