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Add ChatSpatial to Integrative Toolkit #2

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Expand Up @@ -29,6 +29,7 @@ To provide a distinction between Deep Learning and Machine Learning/Statistical
| ***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 |
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