% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/MultiOmicsBridge-package.R
\docType{package}
\name{MultiOmicsBridge-package}
\alias{MultiOmicsBridge-package}
\alias{MultiOmicsBridge}
\title{MultiOmicsBridge: Integrative Multi-Omics Analysis of Host
Transcriptomics and Gut Microbiome Data}
\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 bridges two complementary biological data layers that,
when analyzed together, reveal insights neither can provide alone.
}
\section{The problem this package solves}{

No single Bioconductor package provides all four critical capabilities
for host-microbiome integration in a unified, microbiome-aware workflow:
\enumerate{
  \item Proper normalization for \strong{compositional microbiome data}
    alongside RNA-seq count data.
  \item \strong{Joint dimensionality reduction} identifying shared
    variation patterns between the two data layers.
  \item \strong{Multi-omics biomarker selection} identifying which host
    genes and which microbial taxa jointly predict disease status.
  \item An \strong{integrated diagnostic classifier} demonstrating
    the added value of combining both data types over either alone.
}
MultiOmicsBridge provides all four in a single, opinionated pipeline.
}

\section{Five analysis modules}{

\describe{
  \item{Module 1 — Data Harmonization}{
    \code{\link{loadHostData}}, \code{\link{loadMicrobiomeData}},
    \code{\link{matchSamples}}: Import, normalize, and match paired
    omics data into a \code{MultiAssayExperiment}.}
  \item{Module 2 — Joint Dimensionality Reduction}{
    \code{\link{jointDimReduction}}: Sparse multi-block PLS-DA
    (DIABLO) identifying correlated features across data blocks.}
  \item{Module 3 — Biomarker Discovery}{
    \code{\link{biomarkerDiscovery}}: Sparse feature loadings and
    cross-omics correlation networks for multi-omics biomarker ranking.}
  \item{Module 4 — Diagnostic Classification}{
    \code{\link{diagnosticClassifier}}: Host-only, microbiome-only,
    and joint Random Forest classifiers with stratified k-fold cross-validation.}
  \item{Module 5 — Visualization and Reporting}{
    \code{\link{plotIntegration}}, \code{\link{plotBiomarkerNetwork}},
    \code{\link{plotClassifierComparison}}, \code{\link{plotSankey}},
    \code{\link{generateReport}}.}
}
}

\section{Main functions}{

\describe{
  \item{\code{\link{loadHostData}}}{Import and voom-normalize bulk
    RNA-seq count data.}
  \item{\code{\link{loadMicrobiomeData}}}{Import and CLR-transform
    microbiome taxa table data.}
  \item{\code{\link{matchSamples}}}{Match paired samples across omics
    layers into a \code{MultiAssayExperiment}.}
  \item{\code{\link{jointDimReduction}}}{Run DIABLO joint
    dimensionality reduction.}
  \item{\code{\link{biomarkerDiscovery}}}{Identify ranked multi-omics
    biomarkers.}
  \item{\code{\link{diagnosticClassifier}}}{Train and compare
    single-omics and joint diagnostic classifiers.}
  \item{\code{\link{MultiOmicsBridgeAnalysis}}}{One-call wrapper for
    the complete analysis pipeline.}
}
}

\section{Complex disease contexts}{

The package is designed as a generalized framework and
validated on tuberculosis, HIV antiretroviral therapy, and inflammatory
bowel disease datasets. By providing a standardized, accessible
workflow, MultiOmicsBridge lowers the barrier to multi-omics integration
for researchers working across various disease
contexts.
}

\references{
Rohart F et al. (2017). mixOmics: An R package for 'omics feature
selection and multiple data integration. \emph{PLoS Comput Biol},
13(11), e1005752.

Reel PS et al. (2021). Using machine learning approaches for
multi-omics data analysis: A review.
\emph{Biotechnol Adv}, 49, 107739.

Franzosa EA et al. (2019). Gut microbiome structure and metabolic
activity in inflammatory bowel disease. \emph{Nature Microbiology},
4, 293-305.
}
\seealso{
Useful links:
\itemize{
  \item \url{https://github.com/SubhadipJana1409/MultiOmicsBridge}
  \item Report bugs at \url{https://github.com/SubhadipJana1409/MultiOmicsBridge/issues}
}

}
\author{
\strong{Maintainer}: Subhadip Jana \email{subhadipjana1409@gmail.com} (\href{https://orcid.org/0009-0003-7860-2853}{ORCID}) [funder]

Authors:
\itemize{
  \item Subhadip Jana \email{subhadipjana1409@gmail.com} (\href{https://orcid.org/0009-0003-7860-2853}{ORCID}) [funder]
}

}
