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cell-communication

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Infers ligand-receptor cell-cell communication from scRNA-seq with a consensus-first workflow (LIANA), plus CellPhoneDB specificity tests, CellChat pathway probabilities, and NicheNet downstream ligand-activity. Use when ranking ligand-receptor interactions between cell types, comparing communication across conditions, asking which ligand drives a receiver response, or deciding which CCC method and resource to trust.

When to use

• ranking ligand-receptor interactions between cell types
• comparing communication across conditions
• identifying which ligand drives a receiver response
• assessing interaction specificity
• evaluating downstream ligand-activity
• deciding which CCC method and resource to trust

When not to use

• proving direct signaling
• analyzing mouse data with CellPhoneDB
• using pure magnitude scores alone as communication proof
• de-novo who-talks-to-whom analysis with NicheNet

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