iflow-mcp_scmcphub-scmcp

# SCMCP An MCP server for scRNA-Seq analysis with natural language! ## 🪩 What can it do? - **IO module**: Read and write scRNA-Seq data with natural language - **Preprocessing module**: Filtering, quality control, normalization, scaling, highly-variable genes, PCA, Neighbors,... - **Tool module**: Clustering, differential expression, etc. - **Plotting module**: Violin plots, heatmaps, dotplots - **Cell-cell communication analysis** - **Pseudotime analysis** - **Enrichment analysis** ## ❓ Who is this for? - Anyone who wants to do scRNA-Seq analysis using natural language! - Agent developers who want to call scanpy's functions for their applications ## 🌐 Where to use it? You can use scmcp in most AI clients, plugins, or agent frameworks that support the MCP: - AI clients, like Cherry Studio - Plugins, like Cline - Agent frameworks, like Agno ## 📚 Documentation scmcphub's complete documentation is available at https://docs.scmcphub.org ## 🎬 Demo A demo showing scRNA-Seq cell cluster analysis in an AI client Cherry Studio using natural language based on scmcp: https://github.com/user-attachments/assets/93a8fcd8-aa38-4875-a147-a5eeff22a559 ## 🏎️ Quickstart ### Install Install from PyPI: ```bash pip install scmcp ``` You can test it by running: ```bash scmcp run ``` ## 🚀 Running Modes SCMCP provides two distinct run modes to accommodate different user needs and preferences: ### 1. Tool Mode In tool mode, SCMCP provides a curated set of predefined functions that the LLM can select and execute. **Advantages:** - **Stable**: Predefined functions ensure consistent and reliable execution - **Predictable**: Known behavior and expected outputs - **Safe**: Controlled environment with validated operations **Disadvantages:** - **Limited flexibility**: Restricted to available predefined functions; you need to define new tools when you need customization functions #### Usage Running in terminal: ```bash scmcp run --run-mode tool ``` Configure MCP cli…