Provides deep probabilistic analysis tools for single-cell omics data using scvi-tools, including SCVI for scRNA-seq modeling, SCANVI for cell type annotation, TOTALVI for RNA/protein analysis, and PEAKVI for scATAC-seq analysis.
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!
๐ฏ 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
๐ฆ Installation
๐ Quick Start
๐ง Configuration for Claude Desktop
๐ ๏ธ 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
๐ Example Usage
Basic SCVI workflow:
SCANVI cell type annotation:
๐ License
MIT License
๐ Related Projects
This server cannot be installed
local-only server
The server can only run on the client's local machine because it depends on local resources.
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.