bio-multi-omics-microbiome-metabolomics

What problem does it solve?

Integrate paired microbiome (16S/shotgun) and metabolomics datasets to reveal microbe–metabolite interactions, quantify SCFAs and bile acids, and map tryptophan pathway activity for biological interpretation and downstream modeling.

Core Features & Use Cases

• Co-occurrence modeling and correlation analysis: Prepares BIOM or tabular inputs, applies CLR to compositional taxa and log transforms to metabolites, computes Spearman correlations with FDR correction, and ranks associations using mmvec neural co-occurrence probabilities.
• Targeted assay workflows and pathway scoring: Guides SCFA calibration and internal standard normalization, classifies and summarizes bile acid groups, and computes tryptophan pathway branch scores and the kynurenine-to-tryptophan ratio (KTR).
• Multi-omics integration & visualization: Demonstrates sparse PLS (mixOmics) for feature selection, generates paired heatmaps and correlation networks, and exports ranked microbe-metabolite pairs for follow-up experiments.
• Use case: Match fecal 16S abundance to targeted LC-MS bile acid profiles to identify taxa associated with secondary bile acid production and visualize robust associations for hypothesis generation.

Quick Start

Integrate your sample-matched OTU/ASV table and metabolite concentration matrix to compute CLR-transformed taxa, log-transform metabolites, run mmvec or sPLS to identify top microbe-metabolite associations, and export the ranked results.