MultiOmicsBridge
This is the development version of MultiOmicsBridge; to use it, please install the devel version of Bioconductor.
Integrative Multi-Omics Analysis of Host Transcriptomics and Gut Microbiome Data
Bioconductor version: Development (3.24)
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.
Author: Subhadip Jana [aut, cre, fnd]
Maintainer: Subhadip Jana <subhadipjana1409 at gmail.com>
citation("MultiOmicsBridge")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("MultiOmicsBridge")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MultiOmicsBridge")| Integrative Multi-Omics Analysis with MultiOmicsBridge | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, DimensionReduction, FeatureExtraction, GeneExpression, Metagenomics, Microbiome, MultipleComparison, Network, Normalization, QualityControl, Sequencing, Software, StatisticalMethod, Transcriptomics, Visualization, WorkflowStep |
| Version | 0.99.1 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | SummarizedExperiment, MultiAssayExperiment, S4Vectors, BiocParallel, limma, edgeR, mixOmics, grid, methods, stats, utils, ggplot2, rlang, ranger, pROC, ggrepel |
| System Requirements | |
| URL | https://github.com/SubhadipJana1409/MultiOmicsBridge |
| Bug Reports | https://github.com/SubhadipJana1409/MultiOmicsBridge/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), withr, curatedMetagenomicData, GEOquery |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MultiOmicsBridge_0.99.1.tar.gz |
| Windows Binary (x86_64) | MultiOmicsBridge_0.99.1.zip |
| macOS Binary (big-sur-x86_64) | MultiOmicsBridge_0.99.1.tgz |
| macOS Binary (sonoma-arm64) | MultiOmicsBridge_0.99.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MultiOmicsBridge |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MultiOmicsBridge |
| Bioc Package Browser | https://code.bioconductor.org/browse/MultiOmicsBridge/ |
| Package Short Url | https://bioconductor.org/packages/MultiOmicsBridge/ |
| Package Downloads Report | Download Stats |