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 (>= 4.6.0)
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
git_url: https://git.bioconductor.org/packages/MultiOmicsBridge
git_branch: devel
git_last_commit: a50579b
git_last_commit_date: 2026-07-05
Repository: Bioconductor 3.24
Date/Publication: 2026-07-09
NeedsCompilation: no
Packaged: 2026-07-09 22:12:44 UTC; biocbuild
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; ; 2026-07-10 05:58:37 UTC; unix
