scRNA–Metabolomics Integrator
Bring your single-cell RNA and metabolomics data together: which cell types could be making or using the metabolites that changed, do their enzymes move in the same direction, and which pathways tie the two layers together?
Runs in your browser · no upload · open Human-GEM / Mouse-GEM networkLoading this browser tool…
How to use it
1. Choose the species and load a single-cell table (cell-type averages, pseudobulk per sample and cell type, or a per-cell-type differential expression table) and a metabolomics table (abundance matrix with sample metadata, or a differential table with HMDB/KEGG IDs where you have them). 2. Check the inputs, pick the two conditions to compare and run. 3. Read the plain-language findings, then the candidate-source heatmap, concordance, pathway and correlation tabs. Every table exports as CSV, plots as SVG/PNG, and the full result as JSON with a methods paragraph you can adapt.
What it computes
Each metabolite is linked to the genes of reactions that make it, use it or transport it in the Human-GEM or Mouse-GEM genome-scale metabolic model. For every cell type the tool scores how enriched those enzymes are relative to other cell types and, when conditions are available, whether they change in the direction that would explain the metabolite change. Replicate-level tests are used when you supply pseudobulk samples; otherwise calibrated gene-set permutations. Pathway (subsystem) over-representation and matched-sample enzyme–metabolite correlations add context. All p-values are Benjamini–Hochberg adjusted.
Limits
Transcript levels are not enzyme activity or flux, and blood or tissue metabolites integrate many cell types, diet, microbiota and other organs. Treat the output as ranked hypotheses for targeted experiments such as sorted-cell metabolomics, isotope tracing or genetic perturbation. Reaction directions are generic model annotations. The synthetic example contains planted effects and is not experimental data.
Keep your work
Nothing is stored or uploaded; reloading clears the analysis. Export CSV, SVG/PNG, JSON and the methods text before closing the page.
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