Package: MultiOmicsBridge
Type: Package
Title: Integrative Multi-Omics Analysis of Host Transcriptomics and Gut
        Microbiome Data
Version: 0.99.1
Authors@R: c(
    person("Subhadip", "Jana", role = c("aut", "cre", "fnd"),
           email = "subhadipjana1409@gmail.com",
           comment = c(ORCID = "0009-0003-7860-2853")))
Description: MultiOmicsBridge provides an end-to-end, reproducible
        computational framework for integrative analysis of paired host
        transcriptomics (bulk RNA-seq) and gut microbiome (16S rRNA or
        shotgun metagenomics) data. The package addresses the lack of a
        unified Bioconductor workflow for this pairing by implementing
        five modules: (1) data harmonization and normalization with CLR
        transformation for microbiome compositional data and TMM/voom
        for RNA-seq; (2) joint dimensionality reduction via sparse
        multi-block PLS-DA (DIABLO); (3) multi-omics biomarker
        discovery through cross-omics correlation networks and sparse
        feature loadings; (4) integrated diagnostic classification
        comparing host-only, microbiome-only, and joint Random Forest
        models with stratified cross-validation; and (5)
        publication-quality visualization of integration results,
        biomarker networks, classifier comparisons, and feature flow
        diagrams. All functions operate natively on
        SummarizedExperiment and MultiAssayExperiment objects and
        return a structured MOBResult S4 object. The package is
        validated on inflammatory bowel disease multi-omics data and
        designed with complex disease contexts (tuberculosis, HIV, EED)
        in mind.
License: MIT + file LICENSE
URL: https://github.com/SubhadipJana1409/MultiOmicsBridge
BugReports: https://github.com/SubhadipJana1409/MultiOmicsBridge/issues
biocViews: GeneExpression, Metagenomics, Classification,
        DimensionReduction, Normalization, StatisticalMethod,
        Sequencing, Microbiome, Transcriptomics, WorkflowStep,
        MultipleComparison, FeatureExtraction, Network, Visualization,
        QualityControl
Encoding: UTF-8
Depends: R (>= 4.5.0)
Imports: SummarizedExperiment, MultiAssayExperiment, S4Vectors,
        BiocParallel, limma, edgeR, mixOmics, grid, methods, stats,
        utils, ggplot2, rlang, ranger, pROC, ggrepel
Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), withr,
        curatedMetagenomicData, GEOquery
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake libfreetype6-dev libglpk-dev libglu1-mesa-dev
        make texlive libicu-dev libpng-dev libuv1-dev libxml2-dev
        libgl1-mesa-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-07-05 17:46:43 UTC
RemoteUrl: https://github.com/bioc/MultiOmicsBridge
RemoteRef: HEAD
RemoteSha: a50579b75abec231246c8f79cefa6b5209f1071e
NeedsCompilation: no
Packaged: 2026-07-11 15:44:39 UTC; root
Author: Subhadip Jana [aut, cre, fnd] (ORCID:
    <https://orcid.org/0009-0003-7860-2853>)
Maintainer: Subhadip Jana <subhadipjana1409@gmail.com>
Built: R 4.6.1; ; 2026-07-11 15:56:44 UTC; windows
