ChatSpatial
Active·★ 45·MIT·Updated 2026-10-20
ChatSpatial is an MCP server that simplifies complex spatial transcriptomics analysis tasks using natural language commands. It replaces dozens of lines of Python code with simple English prompts, making advanced bioinformatics accessible.
#Spatial Transcriptomics#Natural Language Processing#Bioinformatics#AI Agent#Genomics#Model Context Protocol#Python#Single-cell Analysis
01
Features
01Natural language interface for spatial transcriptomics analysis.
02Supports over 60 methods across 15 categories for spatial analysis (e.g., Spatial Domains, Deconvolution, Cell Communication).
03Compatible with various spatial omics technologies including 10x Visium, Xenium, Slide-seq v2, MERFISH, seqFISH.
04Works with any Model Context Protocol (MCP)-compatible client (e.g., Claude, OpenCode, Codex).
05Significantly reduces code complexity, transforming multi-line scripts into single-line prompts.
02
Compatibility
Python
Runtime
Verified via docs
Python 3.11+
Version
Verified via docs
Model Context Protocol (MCP)
Protocol
Verified via docs
03
Quick start
1
$ python3 -m venv venv
2
$ source venv/bin/activate
3
$ uv pip install chatspatial
04
Use cases
↳Loading spatial data and visualizing tissue structures.
↳Identifying spatial domains using various algorithms like SpaGCN.
↳Finding spatially variable genes and creating heatmaps.
↳Performing advanced analyses such as cell type deconvolution, cell communication, and trajectory analysis via natural language.
05
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