LIANA-MCP

MCP server that exposes the Python LIANA cell-cell communication workflow as natural-language tools — run multiple ligand-receptor methods, aggregate their ranks, and plot the results.

   
Type MCP server
Supplier scmcphub
Availability GA — v0.4.0 (2025-06-27)
Pricing Free / OSS — BSD-3-Clause (per the scmcphub ecosystem; per-repo LICENSE file not separately confirmed)
Capabilities Read/Write — runs analysis on a loaded AnnData object and writes plots

How to install

Install the package first (required before any registration snippet below works):

pip install liana-mcp
  • Claude Code — stdio (recommended; Claude Code launches the process itself, so do not run liana-mcp run separately): 
    claude mcp add --transport stdio liana -- liana-mcp run
  • Claude Desktop — add to claude_desktop_config.json: 
    {
  "mcpServers": {
    "liana": { "command": "liana-mcp", "args": ["run"] }
  }
}
  • HTTP transport (long-lived service — keep it running in its own terminal; not needed for the stdio setups above): 
    liana-mcp run --transport shttp --port 8000

To verify the install before registering, run liana-mcp run once and Ctrl-C after it boots — for stdio use the host launches it for you.

What it does

  • ls_ccc_method — list available cell-cell communication methods
  • communicate — run ligand-receptor inference (CellPhoneDB, CellChat, Connectome, NATMI, …)
  • rank_aggregate — aggregate ligand-receptor scores across methods
  • circle_plot — circular network visualization
  • ccc_dotplot — dotplot of communication events

Primary use cases: Natural-language cell-cell communication inference, multi-method ligand-receptor ranking, communication-network plotting.

Notes

Built on liana-py. Part of the scmcphub single-cell ecosystem alongside scanpy-mcp, cellrank-mcp, and decoupler-mcp — typically run together on a shared AnnData object. For an R-based alternative to ligand-receptor inference, see the CellChat skill.

Sources

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