CellRank-MCP

MCP server that exposes the CellRank cell-fate workflow as natural-language tools — build kernels, fit a GPCCA estimator, predict initial/terminal states, and compute fate probabilities.

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

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

What it does

  • create_kernel / compute_transition_matrix — build a kernel and its cell-to-cell transition matrix
  • create_and_fit_gpcca — fit the GPCCA estimator
  • predict_terminal_states / predict_initial_states — identify macrostates
  • compute_fate_probabilities — per-cell fate probabilities toward terminal states
  • kernel_projection / circular_projection — trajectory visualizations

Primary use cases: Cell-fate and trajectory modeling, terminal/initial state discovery, fate-probability mapping for developmental single-cell data.

Notes

Built on CellRank. Part of the scmcphub single-cell ecosystem alongside scanpy-mcp, liana-mcp, and decoupler-mcp — typically run together on a shared AnnData object. RNA-velocity kernels require velocity estimates (e.g., from scVelo) precomputed on the object.

Sources

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