# scvi-tools MCP Server

> Use this tool when you need to perform complex single-cell omics data analysis using natural language inputs, solving problems such as cell type annotation, multi-modal data integration, and gene expression analysis. It takes in natural language queries and omics data as inputs, and outputs probabilistic analysis results. Ideal for researchers and bioinformaticians working with single-cell RNA sequencing, proteomics, or ATAC sequencing data.

Canonical page: https://skillsregistry.net/skills/hyennnnnnn-scvi-mcp  
JSON: https://api.skillsregistry.net/v1/skills/hyennnnnnn-scvi-mcp

## Description

Enables deep probabilistic analysis of single-cell omics data using scvi-tools through natural language. Supports SCVI for scRNA-seq analysis, SCANVI for cell type annotation, TOTALVI for multi-modal RNA/protein data, and PEAKVI for scATAC-seq analysis.

## Trust

- **Trust score (0–1):** 1.00
- **Verification tier:** verified
- **Last scanned:** 2026-09-19

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** other
- **Updated:** 2026-09-19

## Source

- **Source listing:** [Glama](https://glama.ai/mcp/servers/smcixm2omr)
- **Repository:** <https://github.com/hyennnnnnn/scvi-mcp>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "hyennnnnnn-scvi-mcp"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/hyennnnnnn-scvi-mcp` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/hyennnnnnn-scvi-mcp/pull`

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