Scanpy
SCMCP is an MCP server that provides natural language access to single-cell RNA sequencing analysis through the Scanpy library. Developed by Shenghui Huang, it exposes a comprehensive set of tools organized into modules for input/output operations, preprocessing, visualization, trajectory inference, and utility functions. The server supports both stdio and server-sent events (SSE) transport protocols, making it flexible for different integration scenarios. SCMCP handles AnnData objects internally, allowing users to perform complex bioinformatics workflows like clustering, dimensionality reduction, differential expression analysis, and cell type annotation through conversational interfaces, making it particularly valuable for researchers who want to analyze single-cell data without writing code.
Composite of vulnerability cleanliness, spec conformance, provenance, stability, and usage signals — scanned and weighted by Cognium. Human and agent signals are tracked separately. Last scanned 2026-09-28.
Scan details: Circle-IR · 2026-09-28 · Appeal
View full trust & usage report →Metadata
- Version
- 1.0.0
- Skill type
- atomic
- Execution layer
- mcp-remote
- Category
- search
- Source
- PulseMCP
- Repository
- github.com/huang-sh/scmcp
- Author type
- human
- Last scanned
- 2026-09-28
- Updated
- 2026-09-28
Use via MCP
Resolve Scanpy from your agent
Streamable HTTP transport at https://api.skillsregistry.net/mcp. No auth for read tools. Discovery: .well-known/mcp.json.
One command in your shell — Claude Code wires it up and verifies the connection. Run /mcp in any session to confirm.
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp--scope user for --scope project to commit it to .mcp.json.