scvi-tools MCP Server

An MCP (Model Context Protocol) server for deep probabilistic analysis of single-cell omics data using scvi-tools with natural language!

🎯 What can it do?

SCVI: Deep generative modeling for scRNA-seq
- Latent representation extraction
- Normalized expression
- Differential expression analysis
- Batch effect correction
SCANVI: Semi-supervised cell type annotation
- Transfer learning from labeled to unlabeled cells
- Cell type prediction
TOTALVI: Joint RNA and protein (CITE-seq) analysis
- Multi-modal integration
- Protein expression denoising
PEAKVI: scATAC-seq analysis
- Chromatin accessibility
- Differential accessibility

📦 Installation

cd /path/to/scvi-mcp python3 -m venv venv source venv/bin/activate pip install -e .

🚀 Quick Start

scvi-mcp run --data /path/to/data.h5ad

🔧 Configuration for Claude Desktop

{ "mcpServers": { "scvi": { "command": "/path/to/scvi-mcp/venv/bin/python", "args": ["-m", "scvi_mcp", "run", "--data", "/path/to/data.h5ad"] } } }

🛠️ Available Tools (22 tools)

SCVI (8 tools)

scvi_setup_anndata, scvi_create_model, scvi_train_model
scvi_get_latent_representation, scvi_get_normalized_expression
scvi_differential_expression, scvi_save_model, scvi_load_model

SCANVI (4 tools)

scanvi_setup_anndata, scanvi_create_model
scanvi_from_scvi_model, scanvi_predict

TOTALVI (3 tools)

totalvi_setup_anndata, totalvi_create_model
totalvi_get_protein_foreground_prob

PEAKVI (3 tools)

peakvi_setup_anndata, peakvi_create_model
peakvi_differential_accessibility

Common (2 tools)

scvi_get_elbo, scvi_get_reconstruction_error

📝 Example Usage

Basic SCVI workflow:

1. "Setup my data for SCVI analysis with batch correction" 2. "Create an SCVI model with 10 latent dimensions" 3. "Train the SCVI model" 4. "Extract the latent representation and save it to X_scVI" 5. "Run differential expression between cell types"

SCANVI cell type annotation:

1. "Setup SCANVI with cell_type labels, mark Unknown as unlabeled" 2. "Create SCANVI model from my trained SCVI model" 3. "Train SCANVI and predict cell types"