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 | ***4. Spatial Clustering***               | [spaGCN](https://github.com/jianhuupenn/SpaGCN)                       | spaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network | Python | 2021 | J. Hu, X. Li, K. Coleman, A. Schroeder, N. Ma, D. J. Irwin, E. B. Lee, R. T. Shinohara, and M. Li, “spaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network,” Nature Methods 18, 1342–1351 (2021). |                  |
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 | ***5. Integrative Tookit***               | [GLUER](https://github.com/software-github/GLUER)                       | GLUER: integrative analysis of multi-omics and imaging data at single-cell resolution by deep neural networks | Python (TensorFlow) | 2021 | GLUER: integrative analysis of single-cell omics and imaging data by deep neural network. Tao Peng, Gregory M. Chen, KaiTan. bioRxiv 2021.01.25.427845; doi: https://doi.org/10.1101/2021.01.25.427845                                                |                  |
+| ***5. Integrative Tookit***               | [ChatSpatial](https://github.com/cafferychen777/ChatSpatial)                       | ChatSpatial: MCP server enabling spatial transcriptomics analysis via natural language | Python | 2025 | MCP server integrating 60+ methods including SpaGCN, Cell2location, LIANA+, CellRank for spatial domains, deconvolution, cell communication, and trajectory analysis. [Docs](https://cafferychen777.github.io/ChatSpatial/)                                                |                  |
 # Machine Learning/Statistical Approaches
 
 | Stage/Category                             | Model (with GitHub Link)                                                | Title of Paper                                                                                                | Language            | Year | Reference                                                                                                                                                                                                                                             | Additional Notes |