cellxgene-mcp
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The CELLxGENE Census MCP Server provides access to a comprehensive collection of single-cell RNA sequencing data, enabling researchers to query and analyze cell and gene metadata efficiently.
The CELLxGENE Census MCP Server is a specialized server designed to facilitate access to the CZ CELLxGENE Discover Census, a vast repository of single-cell RNA sequencing data. This server allows researchers to explore and analyze cell and gene metadata across various organisms, primarily focusing on human and mouse data. With its memory-efficient design, the server supports flexible filtering and querying capabilities, enabling users to obtain data slice summaries without the need to download large datasets. The server is built to handle complex queries while maintaining performance, making it an invaluable tool for researchers in the field of genomics and bioinformatics. By leveraging the Model Context Protocol, the server ensures seamless integration with MCP clients, providing a robust platform for data exploration and analysis.
Features
- Query cell metadata to explore cell types, tissues, diseases, and other annotations.
- Query gene metadata to search genes and their annotations across the Census.
- Get data slice summaries to obtain overview statistics without downloading full matrices.
- Use flexible filtering with pandas-style queries to filter cells and genes.
- Access multi-organism data from human and mouse with built-in memory efficiency.
Tools
cellxgene_get_census_info
Get information about available Census versions and supported organisms.
cellxgene_get_obs_metadata
Query cell (observation) metadata from the Census.
cellxgene_get_var_metadata
Query gene (variable) metadata from the Census.
cellxgene_get_data_slice
Get a summary of a data slice from the Census.