import scanpy as sc
import squidpy as sq
adata = sc.read_h5ad("data.h5ad")
sc.pp.filter_cells(adata, min_genes=200)
sc.pp.normalize_total(adata)
sc.pp.log1p(adata)
sc.pp.highly_variable_genes(adata)
sc.tl.pca(adata)
sc.pp.neighbors(adata)
# ... 40 more lines |
|
# Install
pip install chatspatial
# Configure (use your venv Python path)
claude mcp add chatspatial /path/to/venv/bin/python -- -m chatspatial serverSee Installation Guide for detailed setup including virtual environments and all MCP clients.
Load /path/to/spatial_data.h5ad and show me the tissue structure
Identify spatial domains using SpaGCN
Find spatially variable genes and create a heatmap
| Category | Methods |
|---|---|
| Spatial Domains | SpaGCN, STAGATE, GraphST, Leiden, Louvain |
| Deconvolution | FlashDeconv, Cell2location, RCTD, DestVI, Stereoscope, SPOTlight, Tangram, CARD |
| Cell Communication | LIANA+, CellPhoneDB, CellChat, FastCCC |
| Cell Type Annotation | Tangram, scANVI, CellAssign, mLLMCelltype, scType, SingleR |
| Trajectory & Velocity | CellRank, Palantir, DPT, scVelo, VeloVI |
| Spatial Statistics | Moran's I, Local Moran, Geary's C, Getis-Ord Gi*, Ripley's K, Neighborhood Enrichment |
| Enrichment | GSEA, ORA, Enrichr, ssGSEA, Spatial EnrichMap |
| Spatial Genes | SpatialDE, SPARK-X |
| Integration | Harmony, BBKNN, Scanorama, scVI |
| Other | CNV Analysis, Spatial Registration |
60+ methods across 15 categories. Supports 10x Visium, Xenium, Slide-seq v2, MERFISH, seqFISH.
| Guide | Description |
|---|---|
| Installation | Virtual environment setup, all platforms |
| Quick Start | 5-minute first analysis |
| Examples | Step-by-step workflows |
| Methods Reference | All 20 tools with parameters |
| Full Docs | Complete reference |
@software{chatspatial2025,
title={ChatSpatial: Agentic Workflow for Spatial Transcriptomics},
author={Chen Yang and Xianyang Zhang and Jun Chen},
year={2025},
url={https://github.com/cafferychen777/ChatSpatial}
}