# cafferychen777/ChatSpatial

Source: https://glimind.com/server/awesome%2Fcafferychen777%2Fchatspatial
Registry id: `awesome/cafferychen777/chatspatial`
Status: unknown

## Tools (16)

- `analyze_cnv`: Analyze copy number variations using InferCNVPy or Numbat
- `analyze_communication`: Analyze cell-cell communication using LIANA+, CellPhoneDB, CellChat, or FastCCC
- `annotate_cell_types`: Annotate cell types using Tangram, scANVI, CellAssign, mLLMCelltype, scType, or SingleR
- `compute_velocity`: Compute RNA velocity using scVelo or VeloVI
- `deconvolve`: Perform cell-type deconvolution using methods like FlashDeconv, Cell2location, RCTD, DestVI, Stereoscope, SPOTlight, Tangram, or CARD
- `differential_expression`: Perform differential expression analysis using Wilcoxon, t-test, Logistic Regression, or pyDESeq2
- `enrichment_analysis`: Perform enrichment analysis using GSEA, ORA, Enrichr, ssGSEA, or Spatial EnrichMap
- `find_spatially_variable_genes`: Identify spatially variable genes using SpatialDE, SPARK-X, or FlashS
- `identify_spatial_domains`: Identify spatial domains using methods like SpaGCN, STAGATE, GraphST, BANKSY, AESTETIK, Leiden, or Louvain
- `infer_trajectory`: Infer trajectories using CellRank, Palantir, or DPT
- `integrate_samples`: Integrate multiple samples using Harmony, BBKNN, Scanorama, or scVI
- `load_data`: Load spatial transcriptomics data from an h5ad file
- `preprocess`: Preprocess data including QC, normalization, HVG selection, PCA, and neighbor computation
- `register_spatial`: Register spatial data using PASTE or STalign
- `spatial_statistics`: Compute spatial statistics including Moran's I, Geary's C, Ripley's K, co-occurrence, and others
- `visualize`: Generate spatial plots, embedding plots, or gene expression overlays

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