# Cafferychen777 Chatspatial MCP server

Source: https://glimind.com/server/mcp-registry%2Fio.github.cafferychen777%2Fchatspatial
Registry id: `mcp-registry/io.github.cafferychen777/chatspatial`
Status: unknown

## Install

```json
{
  "mcpServers": {
    "cafferychen777-chatspatial-mcp-server": {
      "command": "uvx",
      "args": [
        "chatspatial"
      ]
    }
  }
}
```

Claude Code:

```sh
claude mcp add cafferychen777-chatspatial-mcp-server -- uvx chatspatial
```

## Tools (16)

- `annotate_cell_types`: Annotate cell types using Tangram, scANVI, CellAssign, mLLMCelltype, scType, SingleR
- `cell_cell_communication`: Analyze cell-cell communication using LIANA+, CellPhoneDB, CellChat, FastCCC
- `cnv_analysis`: Perform CNV analysis using InferCNVPy, Numbat
- `deconvolve`: Perform cell type deconvolution using methods like FlashDeconv, Cell2location, RCTD, DestVI, Stereoscope, SPOTlight, Tangram, CARD
- `differential_expression`: Perform differential expression analysis using Wilcoxon, t-test, Logistic Regression, pyDESeq2
- `enrichment_analysis`: Perform enrichment analysis using GSEA, ORA, Enrichr, ssGSEA, Spatial EnrichMap
- `find_spatially_variable_genes`: Identify spatially variable genes using SpatialDE, SPARK-X, FlashS
- `identify_spatial_domains`: Identify spatial domains using methods like SpaGCN, STAGATE, GraphST, BANKSY, AESTETIK, Leiden, Louvain
- `integrate_samples`: Integrate multi-sample data using Harmony, BBKNN, Scanorama, scVI
- `load_data`: Load spatial transcriptomics data from a file path
- `preprocess`: Preprocess data including QC, normalization, HVG selection, PCA, and neighbors
- `rna_velocity`: Compute RNA velocity using scVelo, VeloVI
- `spatial_registration`: Register spatial data using PASTE, STalign
- `spatial_statistics`: Compute spatial statistics like Moran's I, Geary's C, Ripley's K, co-occurrence, neighborhood enrichment
- `trajectory_inference`: Infer trajectories using CellRank, Palantir, DPT
- `visualize`: Create spatial or embedding plots with gene expression overlays

Measured by Glimind (https://glimind.com): MCP handshake + tool list only, no tool is ever called. CC BY 4.0.