{ "_id": "6a281f2ba476d7de6d3c8174", "Package": "MultiOmicsBridge", "Type": "Package", "Title": "Integrative Multi-Omics Analysis of Host Transcriptomics and Gut\nMicrobiome Data", "Version": "0.99.0", "Authors@R": "c(\nperson(\"Subhadip\", \"Jana\", role = c(\"aut\", \"cre\", \"fnd\"),\nemail = \"subhadipjana1409@gmail.com\",\ncomment = c(ORCID = \"0009-0003-7860-2853\")))", "Description": "MultiOmicsBridge provides an end-to-end, reproducible\ncomputational framework for integrative analysis of paired host\ntranscriptomics (bulk RNA-seq) and gut microbiome (16S rRNA or\nshotgun metagenomics) data. The package addresses the lack of a\nunified Bioconductor workflow for this pairing by implementing\nfive modules: (1) data harmonization and normalization with CLR\ntransformation for microbiome compositional data and TMM/voom\nfor RNA-seq; (2) joint dimensionality reduction via sparse\nmulti-block PLS-DA (DIABLO); (3) multi-omics biomarker\ndiscovery through cross-omics correlation networks and sparse\nfeature loadings; (4) integrated diagnostic classification\ncomparing host-only, microbiome-only, and joint Random Forest\nmodels with nested cross-validation; and (5)\npublication-quality visualization of integration results,\nbiomarker networks, classifier comparisons, and feature flow\ndiagrams. All functions operate natively on\nSummarizedExperiment and MultiAssayExperiment objects and\nreturn a structured MOBResult S4 object. The package is\nvalidated on inflammatory bowel disease multi-omics data and\ndesigned with complex disease contexts (tuberculosis, HIV, EED)\nin mind.", "License": "MIT + file LICENSE", "URL": "https://github.com/SubhadipJana1409/MultiOmicsBridge", "BugReports": "https://github.com/SubhadipJana1409/MultiOmicsBridge/issues", "biocViews": "GeneExpression, Metagenomics, Classification,\nDimensionReduction, Normalization, StatisticalMethod,\nSequencing, Microbiome, Transcriptomics, WorkflowStep,\nMultipleComparison, FeatureExtraction, Network, Visualization,\nQualityControl", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "cmake libfreetype6-dev libglpk-dev libglu1-mesa-dev\nmake texlive libicu-dev libpng-dev libuv1-dev libxml2-dev\nlibgl1-mesa-dev zlib1g-dev", "Repository": "https://biocstaging.r-universe.dev", "Date/Publication": "2026-05-12 19:06:31 UTC", "RemoteUrl": 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