Cell-Hub Database: a consolidated multi-species ligand-receptor interaction resource for cell-cell communication analysis
Cell-cell communication analysis by ligand-receptor interaction inference has become a standard component of single-cell transcriptomics workflows. However, existing ligand-receptor databases are fragmented across independent resources with heterogeneous formats, inconsistent gene nomenclature, and limited species coverage, requiring researchers to manually curate and convert interaction data before use. Here we present CellHub Database, a consolidated ligand-receptor interaction resource integrating 10 independently curated source databases (CellChatDB, CellPhoneDB, CellTalkDB, connectomeDB2025, NicheNet, NeuronChatDB, FlyPhoneDB2, cell2cell, PlantPhoneDB, and PlantCellChatDB) into 67,584 curated interactions across 21 species. To our knowledge, this is the first resource to provide CellChat-compatible ligand-receptor databases for Drosophila melanogaster and Caenorhabditis elegans, and the first to consolidate multiple plant ligand-receptor databases into a unified CellChat-native format covering five plant species. The curation pipeline standardizes gene symbol nomenclature per species, resolves cross-source duplicates using a priority system with full provenance tracking, and validates all gene symbols against reference databases. Users can load individual source databases or a pre-merged version, enabling flexible and transparent cell-cell communication analysis. CellHub Database is freely available as CellChat-native RDS files and integrated into Cell-Hub, an open-source R/Shiny application for no-code single-cell RNA sequencing analysis (companion paper).