Abstract | Introduction and Motivation | Why Bioconductor? | Related Bioconductor Packages and Comparison | Using ExpoRiskR with SummarizedExperiment Objects | Creating and Aligning SummarizedExperiment Inputs | Preprocessing SummarizedExperiment-based Data | Network construction and visualization | Exposure perturbation ranking | Exposure feature importance | Risk ROC curve | Integration with Bioconductor Workflows | Summary | Session information
Package: ExpoRiskR 1.1.0
Prem Prashant Chaudhary
ExpoRiskR: Exposure-Aware Multi-Omics Risk Modeling
ExpoRiskR provides tools for exposure-aware multi-omics risk modeling in translational and environmental health studies. The package aligns sample identifiers across exposure and multi-omics blocks, performs lightweight preprocessing, and fits exposure-adjusted association models to build interpretable microbe–metabolite networks. It also computes simple exposure perturbation summaries and generates publication-ready visualizations. Workflows support both matrix-based inputs and SummarizedExperiment objects.
Authors:
ExpoRiskR_1.1.0.tar.gz
ExpoRiskR_1.1.0.zip(r-4.7)ExpoRiskR_1.1.0.zip(r-4.6)ExpoRiskR_1.1.0.zip(r-4.5)
ExpoRiskR_1.1.0.tgz(r-4.6-any)ExpoRiskR_1.1.0.tgz(r-4.5-any)
ExpoRiskR_1.1.0.tar.gz(r-4.7-any)ExpoRiskR_1.1.0.tar.gz(r-4.6-any)
ExpoRiskR_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ExpoRiskR/json (API)
| # Install 'ExpoRiskR' in R: |
| install.packages('ExpoRiskR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ppchaudhary/exporiskr/issues
On BioConductor:ExpoRiskR-1.1.0(bioc 3.24)ExpoRiskR-1.0.0(bioc 3.23)
softwarenetworksystemsbiologymetabolomicsmicrobiomeregression
Last updated from:1e05ac38d5. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 176 | ||
| linux-devel-x86_64 | OK | 324 | ||
| source / vignettes | OK | 266 | ||
| linux-release-x86_64 | OK | 273 | ||
| macos-release-arm64 | OK | 135 | ||
| macos-oldrel-arm64 | OK | 137 | ||
| windows-devel | OK | 186 | ||
| windows-release | OK | 200 | ||
| windows-oldrel | OK | 228 | ||
| wasm-release | OK | 170 |
Exports:align_omicsalign_omics_sebuild_exposure_networkexposure_perturbation_scoregenerate_dummy_exporiskplot_exposure_networkplot_exposure_rankingplot_feature_importanceplot_individual_risk_profileplot_network_stabilityplot_risk_rocprep_omicsprep_omics_se
Dependencies:abindBiobaseBiocGenericsclicpp11DelayedArrayfarvergenericsGenomicRangesggplot2gluegtableigraphIRangesisobandlabelinglatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatspkgconfigR6RColorBrewerrlangS4ArraysS4VectorsS7scalesSeqinfoSparseArraySummarizedExperimentvctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Align exposures and multi-omics blocks by sample ID | align_omics |
| Align two SummarizedExperiment objects and extract exposures from colData | align_omics_se |
| Build an exposure-adjusted microbe-metabolite association network | build_exposure_network |
| Score exposures by network perturbation (leave-one-exposure-out) | exposure_perturbation_score |
| Generate simulated exposure + multi-omics data with a binary outcome | generate_dummy_exporisk |
| Plot exposure-adjusted multi-omics network (bipartite) | plot_exposure_network |
| Plot exposure perturbation ranking | plot_exposure_ranking |
| Plot feature importance for exposures (logistic regression) | plot_feature_importance |
| Plot individual risk profile from exposure model | plot_individual_risk_profile |
| Plot network stability by bootstrap edge overlap | plot_network_stability |
| Plot disease risk stratification ROC curves (MVP) | plot_risk_roc |
| Preprocess exposures and multi-omics blocks for modeling | prep_omics |
| Preprocess SummarizedExperiment-based omics blocks and exposures | prep_omics_se |