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 |
|
Using Claude Code / Codex / OpenCode? Just paste this:
Install ChatSpatial following https://github.com/cafferychen777/ChatSpatial/blob/main/INSTALLATION.md
Manual installation
# Install uv (recommended - handles complex dependencies)
curl -LsSf https://astral.sh/uv/install.sh | sh
# Create environment and install
python3 -m venv venv && source venv/bin/activate
uv pip install chatspatial
# Configure (use your venv Python path)
claude mcp add chatspatial /path/to/venv/bin/python -- -m chatspatial serverWorks with any MCP-compatible client — not just Claude. Use with OpenCode, Codex, or any client supporting Model Context Protocol. Configure your preferred LLM (Qwen, DeepSeek, Doubao, etc.) as the backend.
See 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}
}