About io.github.cafferychen777/chatspatial
io.github.cafferychen777/chatspatial is an MCP server published by cafferychen777 in the Blockchain category: natural language-driven spatial transcriptomics analysis with 60+ methods via MCP.
The repository has 45 stars and 14 forks, with the last commit 2 days ago. Recent commit activity is the strongest signal that reported issues will get attention.
Install
uvx chatspatialpip install chatspatialThis server has no ConduID identity, so agent calls to it are not receipted. Pin the version you install and review the source before granting it credentials.
Ask AI
Ask AI about io.github.cafferychen777/chatspatial
Powered by Claude · Grounded in docs
Security checks
- ✓README presentThe repository ships documentation.
5 checks have not been run yet.
README
ChatSpatial
MCP server for spatial transcriptomics analysis via natural language
ChatSpatial replaces ad-hoc LLM code generation with schema-enforced orchestration. Instead of generating arbitrary scripts, the LLM selects tools and parameters from a curated registry, making spatial transcriptomics workflows more reproducible across sessions and clients.
It exposes 60+ spatial transcriptomics methods as MCP tools, so any MCP-compatible client can analyze data through natural language.
Start Here
- Install ChatSpatial — Installation Guide
- Configure your MCP client — Configuration Guide
- Run your first analysis — Quick Start
Minimal example prompt:
Load /absolute/path/to/spatial_data.h5ad and show me the tissue structure
ChatSpatial works with any MCP-compatible client — Claude Code, Claude Desktop, Codex, OpenCode, and other MCP-capable tools.
Capabilities
60+ methods across 11 categories. Supports 10x Visium, Xenium, Slide-seq v2, MERFISH, seqFISH.
| Category | Methods |
|---|---|
| Spatial Domains | SpaGCN, STAGATE, GraphST, BANKSY, Leiden, Louvain |
| Deconvolution | FlashDeconv, Cell2location, RCTD, DestVI, Stereoscope, SPOTlight, Tangram, CARD |
| Cell Communication | LIANA+, CellPhoneDB, CellChat (cellchat_r), FastCCC |
| Cell Type Annotation | Tangram, scANVI, CellAssign, mLLMCelltype, scType, SingleR |
| Differential Expression | Wilcoxon, t-test, Logistic Regression, pyDESeq2 |
| Trajectory & Velocity | CellRank, Palantir, DPT, scVelo, VeloVI |
| Spatial Statistics | Moran's I, Local Moran, Geary's C, Getis-Ord Gi*, Ripley's K, Co-occurrence, Neighborhood Enrichment, Centrality Scores, Local Join Count, Network Properties |
| Enrichment | GSEA, ORA, Enrichr, ssGSEA, Spatial EnrichMap |
| Spatial Genes | SpatialDE, SPARK-X, FlashS |
| Integration | Harmony, BBKNN, Scanorama, scVI |
| Other | CNV Analysis (InferCNVPy, Numbat), Spatial Registration (PASTE, STalign) |
Documentation
| Guide | Owns |
|---|---|
| Installation | Environment setup, package install, platform notes |
| Quick Start | First successful analysis after setup |
| Concepts | Method selection and analysis reasoning |
| Examples | Prompt recipes and workflow examples |
| Configuration | Exact MCP client configuration syntax |
| Troubleshooting | Symptom → fix guidance |
| Methods Reference | Canonical tool parameters and defaults |
| Full Docs | Complete documentation site |
Citation
If you use ChatSpatial in your research, please cite:
@article{Yang2026.02.26.708361,
author = {Yang, Chen and Zhang, Xianyang and Chen, Jun},
title = {ChatSpatial: Schema-Enforced Agentic Orchestration for Reproducible and Cross-Platform Spatial Transcriptomics},
elocation-id = {2026.02.26.708361},
year = {2026},
doi = {10.64898/2026.02.26.708361},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2026/03/01/2026.02.26.708361},
journal = {bioRxiv}
}
ChatSpatial orchestrates many excellent third-party methods. Please also cite the original tools your analysis used.
Contributing
Documentation improvements, bug reports, and new analysis methods are all welcome. See CONTRIBUTING.md.
README copy captured when this server was indexed; it may lag the repository. The original is authoritative.