{"$schema":"https://wellknown.network/schemas/agent-record-v1.json","schemaVersion":"1","id":"ag_ge2xpx579wym","handle":"iflow-mcp-scmcphub-scmcp","url":"https://wellknown.network/agents/iflow-mcp-scmcphub-scmcp","links":{"self":"https://wellknown.network/agents/iflow-mcp-scmcphub-scmcp/record.json","html":"https://wellknown.network/agents/iflow-mcp-scmcphub-scmcp","markdown":"https://wellknown.network/agents/iflow-mcp-scmcphub-scmcp/record.md","api":"https://wellknown.network/api/v1/agents/iflow-mcp-scmcphub-scmcp","status":"https://wellknown.network/api/v1/agents/iflow-mcp-scmcphub-scmcp/status","claim":"https://wellknown.network/agents/iflow-mcp-scmcphub-scmcp/claim","claimApi":"https://wellknown.network/api/v1/claims","claimDescriptor":"https://wellknown.network/agents/iflow-mcp-scmcphub-scmcp/claim.json","badge":"https://wellknown.network/agents/iflow-mcp-scmcphub-scmcp/badge.svg","openapi":"https://wellknown.network/openapi.json","history":"https://wellknown.network/api/v1/agents/iflow-mcp-scmcphub-scmcp/history","tools":"https://wellknown.network/api/v1/agents/iflow-mcp-scmcphub-scmcp/tools"},"ard":{"identifier":"urn:air::server:iflow-mcp-scmcphub-scmcp","type":"application/mcp-server-card+json"},"kind":"mcp_server","declared":{"name":"iflow-mcp_scmcphub-scmcp","summary":"An MCP server for scRNA-Seq analysis with natural language!","description":"# SCMCP\n\nAn MCP server for scRNA-Seq analysis with natural language!\n\n## 🪩 What can it do?\n\n- **IO module**: Read and write scRNA-Seq data with natural language\n- **Preprocessing module**: Filtering, quality control, normalization, scaling, highly-variable genes, PCA, Neighbors,...\n- **Tool module**: Clustering, differential expression, etc.\n- **Plotting module**: Violin plots, heatmaps, dotplots\n- **Cell-cell communication analysis**\n- **Pseudotime analysis**\n- **Enrichment analysis**\n\n## ❓ Who is this for?\n\n- Anyone who wants to do scRNA-Seq analysis using natural language!\n- Agent developers who want to call scanpy's functions for their applications\n\n## 🌐 Where to use it?\n\nYou can use scmcp in most AI clients, plugins, or agent frameworks that support the MCP:\n\n- AI clients, like Cherry Studio\n- Plugins, like Cline\n- Agent frameworks, like Agno \n\n## 📚 Documentation\n\nscmcphub's complete documentation is available at https://docs.scmcphub.org\n\n## 🎬 Demo\n\nA demo showing scRNA-Seq cell cluster analysis in an AI client Cherry Studio using natural language based on scmcp:\n\nhttps://github.com/user-attachments/assets/93a8fcd8-aa38-4875-a147-a5eeff22a559\n\n## 🏎️ Quickstart\n\n### Install\n\nInstall from PyPI:\n```bash\npip install scmcp\n```\n\nYou can test it by running:\n```bash\nscmcp run\n```\n\n## 🚀 Running Modes\n\nSCMCP provides two distinct run modes to accommodate different user needs and preferences:\n\n### 1. Tool Mode\n\nIn tool mode, SCMCP provides a curated set of predefined functions that the LLM can select and execute.\n\n**Advantages:**\n- **Stable**: Predefined functions ensure consistent and reliable execution\n- **Predictable**: Known behavior and expected outputs\n- **Safe**: Controlled environment with validated operations\n\n**Disadvantages:**\n- **Limited flexibility**: Restricted to available predefined functions; you need to define new tools when you need customization functions\n\n#### Usage\n\nRunning in terminal:\n```bash\nscmcp run --run-mode tool\n```\n\nConfigure MCP cli…","publisher":null,"homepage":"https://docs.scmcphub.org/","repository":"https://github.com/scmcphub/scmcp","version":"0.5.0","license":"BSD 3-Clause License  Copyright (c) 2025, Shenghui  Redistribut…","protocols":["mcp"],"tags":["ai","agent","bioinformatics","llm","mcp","model","context","protocol","scrna-seq","single","cell"],"pricing":null,"endpoints":[{"url":"pypi:iflow-mcp_scmcphub-scmcp","type":"package_pypi","auth":null,"probeable":false}],"skills":null,"tools":null,"extra":null,"attribution":{"kind":"pypi","name":"pypi","license":"pypi","repoUrl":"pypi","summary":"pypi","version":"pypi","description":"pypi","homepageUrl":"pypi"}},"derived":{"capabilities":[{"slug":"dev.terminal","name":"Terminal & Shell","confidence":0.779,"provenance":"derived"}],"categories":["dev"],"language":"en"},"observed":{"status":"unknown","statusReason":"Distributed as a package to run locally; no network endpoint to check.","lastOkAt":null,"lastProbedAt":null,"statusComputedAt":null,"reliability30d":null,"latestObservations":[],"tools":null,"package":{"name":"iflow-mcp_scmcphub-scmcp","registry":"pypi","observedAt":"2026-09-15T20:21:18.511Z","publishedAt":"2026-02-11T10:44:46.047967Z","latestVersion":"0.5.0"},"toolSurface":null,"endpointFacts":[]},"verification":{"claimed":false,"claimedAt":null,"proofs":[]},"provenance":{"sources":[{"source":"pypi","key":"iflow-mcp_scmcphub-scmcp","url":"https://pypi.org/project/iflow-mcp_scmcphub-scmcp/","firstSeenAt":"2026-09-09T21:23:39.537Z","fetchedAt":"2026-09-15T20:19:21.913Z","normalizedAt":"2026-09-15T20:19:21.913Z"}]},"firstSeenAt":"2026-09-09T21:23:39.537Z","updatedAt":"2026-09-15T20:21:18.511Z"}