{"slug":"cafferychen777/chatspatial","name":"ChatSpatial","description":"MCP server for spatial transcriptomics analysis with 60+ integrated methods","category":"other","tags":[],"official":false,"stars":39,"transport":null,"install":null,"tools":[{"name":"load_data","description":"Load spatial transcriptomics data from various platforms (Visium, Xenium, Slide-seq v2, MERFISH, seqFISH)"},{"name":"preprocess","description":"Quality control, normalization, HVG selection, PCA, and neighbor graph construction"},{"name":"spatial_plot","description":"Generate spatial plots of gene expression or metadata"},{"name":"embedding_plot","description":"Generate embedding plots (e.g., UMAP, t-SNE) colored by gene expression or metadata"},{"name":"gene_expression_overlay","description":"Overlay gene expression on spatial coordinates"},{"name":"spatial_domain","description":"Identify spatial domains using methods like SpaGCN, STAGATE, GraphST, BANKSY, Leiden, or Louvain"},{"name":"deconvolution","description":"Perform cell-type deconvolution using FlashDeconv, Cell2location, RCTD, DestVI, Stereoscope, SPOTlight, Tangram, or CARD"},{"name":"cell_cell_communication","description":"Analyze cell-cell communication with LIANA+, CellPhoneDB, CellChat, or FastCCC"},{"name":"cell_type_annotation","description":"Annotate cell types using Tangram, scANVI, CellAssign, mLLMCelltype, scType, or SingleR"},{"name":"differential_expression","description":"Perform differential expression analysis with Wilcoxon, t-test, Logistic Regression, or pyDESeq2"},{"name":"trajectory_inference","description":"Infer developmental trajectories using CellRank, Palantir, or DPT"},{"name":"rna_velocity","description":"Estimate RNA velocity with scVelo or VeloVI"},{"name":"spatial_statistics","description":"Compute spatial statistics including Moran's I, Geary's C, Ripley's K, co-occurrence, neighborhood enrichment, and more"},{"name":"enrichment_analysis","description":"Perform enrichment analysis with GSEA, ORA, Enrichr, ssGSEA, or Spatial EnrichMap"},{"name":"spatially_variable_genes","description":"Identify spatially variable genes using SpatialDE, SPARK-X, or FlashS"},{"name":"multi_sample_integration","description":"Integrate multiple samples with Harmony, BBKNN, Scanorama, or scVI"},{"name":"cnv_analysis","description":"Analyze copy number variations with InferCNVPy or Numbat"},{"name":"spatial_registration","description":"Register spatial data across sections using PASTE or STalign"}],"env_vars":[],"auth_type":"none","github":"https://github.com/cafferychen777/ChatSpatial","homepage":"","server_url":"","status":"active","source":"mcpservers.org","updated_at":"Thu May 28"}