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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 |