scVI-Tools MCP

An MCP (Model Context Protocol) server that gives LLMs structured access to scvi-tools knowledge: model documentation, tutorials, API reference, workflow templates, pretrained Hugging Face Hub models, and community FAQ.

No runtime model execution — pure knowledge layer. Works with Claude Desktop, Cursor, and any MCP-compatible client.

Docs: scvi-tools-mcp.readthedocs.io

---

Quick Start

Claude Desktop

Add to ~/Library/Application Support/Claude/claude_desktop_config.json:

{
  "mcpServers": {
    "scvi-tools": {
      "command": "uvx",
      "args": ["scvi-tools-mcp"]
    }
  }
}

Claude Code (CLI)

claude mcp add scvi-tools-mcp -s user -- uvx scvi-tools-mcp

OpenAI Codex CLI

Add to ~/.codex/config.toml:

[mcp_servers.scvi-tools-mcp]
command = "uvx"
args   = ["scvi-tools-mcp"]

Cursor / Windsurf / other clients

{ "command": "uvx", "args": ["scvi-tools-mcp"] }

Local install

pip install scvi-tools-mcp
scvi-tools-mcp

---

Tools

Tool	Description
recommend_model	Rank models by task and data type — start here
get_model_overview	Full model description, use cases, inputs, outputs
get_model_parameters	Key __init__ and train() parameters with defaults
get_setup_anndata_guide	Exact setup_anndata() call + required obs/var fields
validate_data_requirements	Pass/fail checklist for your AnnData against a model
list_tutorials	Browse tutorials by category
get_tutorial	Paginated tutorial content (code + prose, no outputs)
search_tutorials	Keyword search across all tutorials
get_api_reference	Signature + docstring for any public class or function
search_api	Search public symbols by keyword
get_workflow_template	Step-by-step code template for an analysis task
get_downstream_guide	Guide for DE, clustering, embedding, label transfer
list_hub_models	Browse official scvi-tools Hugging Face Hub models
get_hub_model	Inspect one pretrained HubModel repo
suggest_hub_models	Suggest Hub models for reference/query workflows
list_scviva_models	Browse scviva-tools spatial models (ResolVI, DestVI, …)
get_scviva_model	API reference + user guide for one scviva-tools model
list_scviva_tutorials	Browse scviva-tools tutorials
get_scviva_tutorial	Paginated scviva-tools tutorial content
list_scib_metrics	Browse scib-metrics integration-benchmarking metrics
get_scib_metric	API reference for one scib-metrics metric or benchmark
list_scib_metrics_tutorials	Browse scib-metrics tutorials
get_scib_metrics_tutorial	Paginated scib-metrics tutorial content
get_faq	Curated FAQ from docs, GitHub issues, and Discourse
search_knowledge	Cross-search all knowledge (catch-all)

---

Knowledge Sources

All knowledge is baked into the package as Markdown files at build time. No network calls at tool-call time.

| Directory | Content