Protocol for integrating and interpreting multi-omics data combining unsupervised and supervised data integrating approaches.

Multi-omics integration combines data from transcriptomics, proteomics, and metabolomics to provide insights into biological systems. Here, we present a protocol for integrating and interpreting multi-omics data using unsupervised multi-omics factor analysis (MOFA), supervised projection-based integration (data integration analysis for biomarker discovery using latent components, DIABLO), along with general single-omics analysis techniques and visualizations. We describe steps for data preparation, model construction, and biological interpretation of multi-omics datasets. These approaches identify coordinated molecular changes across biological layers and reveal regulatory mechanisms that drive biological processes. For complete details on the use and execution of this protocol, please refer to Anagho-Mattanovich et al.