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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "MultiOmicsBridge" in publications use:'
type: software
license: MIT
title: 'MultiOmicsBridge: Integrative Multi-Omics Analysis of Host Transcriptomics
  and Gut Microbiome Data'
version: 0.99.0
abstract: '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 nested 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.'
authors:
- family-names: Jana
  given-names: Subhadip
  email: subhadipjana1409@gmail.com
  orcid: https://orcid.org/0009-0003-7860-2853
repository: https://biocstaging.r-universe.dev
repository-code: https://github.com/SubhadipJana1409/MultiOmicsBridge
commit: 569692509f816b3d8aee150c97bacac2f504fe5c
url: https://github.com/SubhadipJana1409/MultiOmicsBridge
date-released: '2026-05-12'
contact:
- family-names: Jana
  given-names: Subhadip
  email: subhadipjana1409@gmail.com
  orcid: https://orcid.org/0009-0003-7860-2853