# Liana-MCP
Natural language interface for scRNA-Seq analysis with Liana through MCP.
## 🪩 What can it do?
- IO module like read and write scRNA-Seq data
- Cell-cell communication method
- Plotting module, circle plot, dotplot
## ❓ Who is this for?
- Anyone who wants to do scRNA-Seq analysis natural language!
- Agent developers who want to call Liana's functions for their applications
## 🌐 Where to use it?
You can use Liana-mcp in most AI clients, plugins, or agent frameworks that support the MCP:
- AI clients, like Cherry Studio
- Plugins, like Cline
- Agent frameworks, like Agno
## 🎬 Demo
A demo showing scRNA-Seq cell cluster analysis in a AI client Cherry Studio using natural language based on Liana-mcp
https://github.com/user-attachments/assets/40fb5bd8-a166-4993-9979-3258ef6646a0
## 📚 Documentation
scmcphub's complete documentation is available at https://docs.scmcphub.org
## 🏎️ Quickstart
### Install
Install from PyPI
```
pip install liana-mcp
```
you can test it by running
```
liana-mcp run
```
#### run liana-mcp locally
Refer to the following configuration in your MCP client:
check path
```
$ which liana
/home/test/bin/liana-mcp
```
```
"mcpServers": {
"liana-mcp": {
"command": "/home/test/bin/liana-mcp",
"args": [
"run"
]
}
}
```
#### run liana-server remotely
Refer to the following configuration in your MCP client:
run it in your server
```
liana-mcp run --transport shttp --port 8000
```
Then configure your MCP client in local AI client, like this:
```
"mcpServers": {
"liana-mcp": {
"url": "http://localhost:8000/mcp"
}
}
```
## 🤝 Contributing
If you have any questions, welcome to submit an issue, or contact me(hsh-me@outlook.com). Contributions to the code are also welcome!
## Citing
If you use liana-mcp in for your research, please consider citing following work:
> Dimitrov D., Schäfer P.S.L, Farr E., Rodriguez Mier P., Lobentanzer S., Badia-i-Mompel P., Dugourd A., Tanevski J., Ramirez Flores R.O. and Saez-Rodriguez J. LIANA+ provides an all-in-one framework for cell–cell communication inference. Nat Cell Biol (2024). https://doi.org/10.1038/s41556-024-01469-w
