Scanpy-MCP
Rank #30,795glama/scmcphub/scanpy-mcp
Provides a natural language interface for scRNA-Seq analysis using the Scanpy library, supporting operations such as data preprocessing, clustering, and visualization. It enables AI agents and clients to perform complex single-cell transcriptomics workflows through the Model Context Protocol.
What you can do with Scanpy-MCP
Scanpy-MCP is a Model Context Protocol (MCP) server published by scmcphub. It ranks #30,795 of 144,396 active servers on MCP Toplist, and its repository has 2 GitHub stars. Scanpy-MCP is listed across 2 registries — Glama and mcp.so, with 5 release tags tracked from its GitHub repository. It was first listed on May 21, 2025 and most recently updated on Jun 27, 2025.
Not verifiedMCP Toplist has not yet written a checked profile for this server, so the paragraph above is assembled from registry data only. The repository README is the authority on what it does.
What Scanpy-MCP can and cannot do
Not verifiedMCP Toplist has not catalogued this server's tools or limitations. The repository README lists them.
What you need before using Scanpy-MCP
The registry listing declares no required environment variables or authentication. This is declared metadata, not a verified install — the repository README is the authority.
Declared by Glama, last synced Oct 16, 2026. Not independently verified by MCP Toplist.
No runtime, credential or payment requirements are recorded for this server beyond the declaration above.
Connect Scanpy-MCP and confirm it works
Install configuration unavailable. No registry publishes a machine-readable install config for this server — follow the repository README.
After adding the config, ask your client to list this server's tools. A tool list confirms the connection; an empty list or an error means the server did not start or needs credentials.
When to choose another server
- SCMCP#13,579
- decoupler-MCP#23,321
- cellrank-mcp#30,794
- biomarker-mcp#31,367
- Infercnv-MCP#35,627
- Liana-MCP#38,362
No task-specific alternatives are catalogued for Scanpy-MCPyet; the list above is its publisher's other servers.
What changed, and when this was checked
- First listed
- May 21, 2025
- Latest release tag
- Jun 27, 2025
- Version history
- 5 release tags tracked (below)
- Requirements evidence
- Declared by Glama, last synced Oct 16, 2026. Not independently verified by MCP Toplist.
- Profile checked
- Not yet — purpose, capabilities and requirements above come from registry data only
- Ranking data as of
- Oct 16, 2026
Do you maintain Scanpy-MCP? to correct or enrich this profile.
GitHub releases (5)
No registry surfaces explicit version metadata for this server. The list below shows release tags from the linked GitHub repository.
| Version | Published |
|---|---|
| v0.5.0 | Jun 27, 2025 |
| v0.4.1 | Jun 1, 2025 |
| v0.4.0 | May 29, 2025 |
| v0.3.2 | May 22, 2025 |
| v0.3.1 | May 21, 2025 |
Ranks ahead of 113,601 of 144,396 servers on MCP Toplist.
Show your rank
Maintain this server? Add the live rank badge to your README — it updates automatically as the leaderboard changes.
[](https://mcptoplist.com/server/glama%2Fscmcphub%2Fscanpy-mcp)<a href="https://mcptoplist.com/server/glama%2Fscmcphub%2Fscanpy-mcp"><img src="https://mcptoplist.com/badge/glama%2Fscmcphub%2Fscanpy-mcp.svg" alt="MCP Toplist: Top 25% of 144,396" /></a>Variants: append ?metric=score or ?metric=stars to the image URL.
Frequently asked questions
- Who maintains Scanpy-MCP?
- Scanpy-MCP is maintained by scmcphub, which publishes 7 MCP servers (31 total versions) tracked on MCP Toplist.
- Is Scanpy-MCP listed on the Official MCP Registry?
- Scanpy-MCP is not on the Official MCP Registry. It is listed on Glama and mcp.so.
- How many versions does Scanpy-MCP have?
- No registry surfaces explicit version metadata for Scanpy-MCP; MCP Toplist tracks 5 release tags from its GitHub repository, most recently published on Jun 27, 2025.
- Where can I find the source code for Scanpy-MCP?
- The source code for Scanpy-MCP is hosted at github.com/scmcphub/scanpy-mcp.
Do you run this server?
Community projects list the MCP servers behind real agents and apps. Publish yours and this page will link to it.