scMetaLink: Single-Cell Metabolite-Mediated Cell Communication Analysis

A comprehensive framework for inferring metabolite-mediated cell-cell communication from single-cell transcriptomic data. scMetaLink integrates metabolite production potential via enzyme expression, metabolite sensing capability via receptor and transporter expression, and secretion potential to construct intercellular metabolic communication networks.

Details

The package provides the following main functions:

• createScMetaLink: Create analysis object from expression data

• inferProduction: Infer metabolite production potential

• inferSensing: Infer metabolite sensing capability

• computeCommunication: Compute cell-cell communication scores

• filterSignificantInteractions: Filter significant interactions

• aggregateByPathway: Aggregate by metabolic pathways

• runScMetaLink: Run complete analysis pipeline

For spatial transcriptomics data:

• createScMetaLinkFromSpatial: Create object from spatial data

• computeSpatialCommunication: Compute spatially-weighted communication

Database

scMetaLink utilizes MetalinksDB, containing:

• 41,894 metabolite-protein interactions

• 1,128 metabolites

• 4,374 proteins/genes

• 157,741 pathway associations

See also

Useful links:

• https://github.com/Zaoqu-Liu/scMetaLink

• https://Zaoqu-Liu.github.io/scMetaLink/

• Report bugs at https://github.com/Zaoqu-Liu/scMetaLink/issues

Author

Zaoqu Liu liuzaoqu@163.com