Document Type
Article
Publication Date
2-3-2026
Identifier
DOI: 10.1093/bioinformatics/btag030; PMCID: PMC12925246
Abstract
SUMMARY: Integrative Module Analysis for Multi-omics Data (iModMix) is a biology-agnostic framework that enables the discovery of novel associations across any type of quantitative abundance data, including but not limited to transcriptomics, proteomics, and metabolomics. Instead of relying on pathway annotations or prior biological knowledge, iModMix constructs data-driven modules using graphical lasso to estimate sparse networks from omics features. These modules are summarized into eigenfeatures and correlated across datasets for horizontal integration, while preserving the distinct feature sets and interpretability of each omics type. iModMix operates directly on matrices containing expression or abundances for a wide range of features, including but not limited to genes, proteins, and metabolites. Because it does not rely on annotations (e.g., KEGG identifiers), it can seamlessly incorporate both identified and unidentified metabolites, addressing a key limitation of many existing metabolomics tools. iModMix is available as a user-friendly R Shiny application requiring no programming expertise (https://imodmix.moffitt.org), and as a Bioconductor R package for advanced users (https://bioconductor.org/packages/release/bioc/html/iModMix.html). The tool includes several public and in-house datasets to illustrate its utility in identifying novel multi-omics relationships in diverse biological contexts.
AVAILABILITY AND IMPLEMENTATION: iModMix is freely available from Bioconductor (https://bioconductor.org/packages/release/bioc/html/iModMix.html), and the example dataset package (iModMixData) is also available from Bioconductor (https://bioconductor.org/packages/release/ data/experiment/html/iModMixData.html). The R package source code and Docker are available from GitHub: https://github.com/biodatalab/iModMix. Shiny application can be accessed at: https://imodmix.moffitt.org.
Journal Title
Bioinformatics (Oxford, England)
Volume
42
Issue
2
MeSH Keywords
Software; Metabolomics; Proteomics; Computational Biology; Humans; Genomics; Gene Expression Profiling; Multiomics
PubMed ID
41555479
Keywords
Software; Metabolomics; Proteomics; Computational Biology; Humans; Genomics; Gene Expression Profiling; Multiomics
Recommended Citation
Narváez-Bandera I, Lui A, Mekonnen YA, et al. iModMix: integrative module analysis for multi-omics data. Bioinformatics. 2026;42(2):btag030. doi:10.1093/bioinformatics/btag030
Comments
Grants and funding
This is an open access article distributed under the terms of the Creative Commons CC BY license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Publisher's Link: https://academic.oup.com/bioinformatics/article/42/2/btag030/8430290?login=false