ChatSpatial

About

ChatSpatial is an agentic workflow orchestration platform designed to eliminate the implementation tax in spatial transcriptomics research. It integrates over 60 state-of-the-art methods from diverse Python and R ecosystems into a unified, conversational interface. Built on the Model Context Protocol (MCP), ChatSpatial empowers human-steered discovery through natural language interactions in clients like Claude Desktop or Claude Code, drastically simplifying complex bioinformatics analysis and accelerating the journey to biological insight.

Key Features

• Analyzes spatial transcriptomics data using natural language conversation via LLM agents
• Eliminates the need for manual coding, data conversion, and complex programming
• Generates publication-ready outputs and visualizations instantly
• Supports diverse spatial data formats including 10x Genomics Visium, Xenium, MERFISH, and H5AD
• 2 GitHub stars
• Integrates 60+ state-of-the-art methods from fragmented Python and R ecosystems

Use Cases

• Finding marker genes, analyzing cell communication, or detecting spatially variable genes without writing any code
• Performing comprehensive spatial transcriptomics analysis, such as identifying spatial domains or deconvolving cell types, using plain English prompts
• Accelerating bioinformatics research by transforming multi-step, complex pipelines into simple conversational commands