Name: Liana-MCP
Author: scmcphub

LABSCO SUMMARY

The analysis you already know, without the notebook around it.

What this removes is the scaffolding: loading, calling the method with the right arguments, and getting a circle plot out. For exploring a clustered dataset conversationally, or for an agent that needs communication inference as one step in a longer pipeline, that is exactly the friction worth removing. It is a wrapper, so the method's assumptions and its limits are LIANA+'s — read them there before you draw a conclusion from an edge on a circle plot.

What it is

An MCP server wrapping LIANA+, the framework for inferring cell-cell communication from single-cell RNA-seq data. It covers reading and writing the data, running the communication inference, and producing the plots the result is normally read from.

What you get

Single-cell data read in and written back out — the IO module
Cell-cell communication inference over the loaded object — the method module
The two plots the results are usually read from: circle plot and dotplot — the plotting module
Use from most clients that speak MCP, including desktop clients, editor plugins and agent frameworks

Requirements

No account and no key — it runs against data on your own machine. pip install liana-mcp, then liana-mcp run starts it over stdio; the client entry points at the absolute path of the installed binary with the run argument. To reach it from another machine, liana-mcp run --transport shttp --port 8000 serves it at http://localhost:8000/mcp. The pyproject name is liana-mcp. Documentation for the scmcphub family is at docs.scmcphub.org. If you publish work using it, the authors ask that you cite the LIANA+ paper.

Setup effort

One command — pip install liana-mcp

See installation options

USE CASES

01

Getting a first look at cell-cell signalling

Load the dataset, run the inference and view the circle plot without writing a notebook.

02

Comparing interactions across cell types

Produce the dotplot over the inferred result and read which ligand-receptor pairs stand out.

03

Adding communication inference to an agent pipeline

Run it over streamable HTTP so a framework can call it as one step among several.

BEFORE YOU INSTALL

What to know first

Requires

pip on PATH

INSTALLATION

Connect your client

Server setup

Configuration file

JSON

{
  "mcpServers": {
    "liana-mcp": {
      "command": "/home/test/bin/liana-mcp",
      "args": [
        "run"
      ]
    }
  }
}

/home/test/bin/liana-mcp is the README's example; yours is the full path of the liana-mcp command that pip install created (the README finds it with which).

pip

TERMINAL

pip install liana-mcp

Liana-MCP