ChatSpatial

Install

Works with Claude Code, Codex, VS Code, Cursor, Windsurf, Claude Desktop. Read the repository before you give any tool access to your data.

npx agentmarket install connector/cafferychen777-chatspatial

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What this server can do and what it asks for, from its tool list, install config and code. Checked Oct 25, 2026.

Tools

13 read · 3 write · 0 delete · 4 not yet classified

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Python package

Tools (20)

Read from the source code; the running server may differ. Descriptions are the server’s own words; hidden characters are shown as [U+…].

• analyze_cell_communication

  Analyze cell-cell communication and ligand-receptor interaction patterns. Args: data_id: Dataset ID params: Required - species, cell_type_key, and method. For mouse with liana, set liana_resource='mouseconsensus'. subset_key + subset_categories restrict the analysis to those observations (e.g. tc_le_region in ['TC', 'LE']).

• analyze_cnv

  Analyze copy number variations (CNVs) in spatial transcriptomics data. Args: data_id: Dataset identifier params: Required - reference_key, reference_categories, and optional method/thresholds. Gene positions missing from adata.var are annotated from bundled Ensembl 110 tables (species: human GRCh38 or mouse GRCm39). exclude_gene_classes removes immunoglobulin, ribosomal, mitochondrial or HLA genes from the CNV input; query_categories restricts CNV clustering to those reference_key categories.

• analyze_enrichment

  Perform gene set enrichment analysis. Args: data_id: Dataset ID params: Required - species must be specified. See EnrichmentParameters for methods and gene_set_database options.

• analyze_spatial_statistics

  Analyze spatial statistics and autocorrelation patterns. Args: data_id: Dataset ID params: Analysis parameters (analysis_type, cluster_key, genes). See SpatialStatisticsParameters for all types. gene_selection='all' computes moran/geary for every gene; the full per-gene table (rank, statistic, p, FDR) is stored at results_key, only top genes are returned.

• analyze_trajectory_data

  Infer cellular trajectories and pseudotime ordering. Args: data_id: Dataset ID params: Trajectory parameters (method, root_cell, spatial_weight, etc.)

• analyze_velocity_data

  Analyze RNA velocity to understand cellular dynamics. Requires 'spliced' and 'unspliced' layers. Args: data_id: Dataset ID params: Velocity parameters (method, scvelo_mode, etc.)

• annotate_cell_types

  Annotate cell types in spatial transcriptomics data. Args: data_id: Dataset ID params: Annotation parameters (method, reference_data_id, cell_type_key, etc.) Note: Reference methods (tangram, scanvi) require reference_data_id to be preprocessed first. Rule-based methods: marker_score labels the groups of cluster_label (e.g. spatial domains) by mean log-normalized marker expression; threshold labels observations by a cutoff on a numeric obs column (e.g. deconvolution_rctd_<cell type>). Both write to output_key.

• compare_conditions

  Compare experimental conditions using pseudobulk differential expression (DESeq2). Args: data_id: Dataset ID params: Required - condition_key, condition1, condition2, sample_key, etc.

• compute_embeddings

  Compute dimensionality reduction (PCA, UMAP), clustering, and neighbor graphs. Args: data_id: Dataset ID params: Embedding parameters (PCA, UMAP, clustering, etc.)

• deconvolve_data

  Deconvolve spatial spots to estimate cell type proportions. Args: data_id: Dataset ID params: Required - method, cell_type_key, reference_data_id. See DeconvolutionParameters for all methods and options.

• export_data

  Export dataset to disk for external script access. Args: data_id: Dataset ID to export path: Custom path (default: ~/.chatspatial/active/{data_id}.h5ad) Returns: Absolute path where data was exported

• find_markers

  Find differentially expressed genes between groups. Args: data_id: Dataset ID params: Required - group_key and optional method, group1/group2, n_top_genes, etc.

• find_spatial_genes

  Identify spatially variable genes. Args: data_id: Dataset ID params: Spatial variable gene parameters (method, n_top_genes, etc.)

• identify_spatial_domains

  Identify spatial domains and tissue architecture. Args: data_id: Dataset ID params: Spatial domain parameters (method, n_domains, resolution, etc.)

• integrate_samples

  Integrate multiple spatial transcriptomics samples into a unified dataset. Args: data_ids: List of dataset IDs to integrate params: Integration parameters (method, batch_key, n_pcs, etc.) batch_correction=False pools the samples without correction (shared genes, counts in layers['counts'], obs and coordinates kept), e.g. to pool sections for analyze_cell_communication.

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Stars

45

Forks

14

Open issues

4

Weekly downloads

311

Last commit

Oct 20, 2026 (19 days ago)

Last release

Oct 20, 2026 (19 days ago)

Last package publish

Oct 20, 2026 (19 days ago)

From GitHub (fetched Oct 24, 2026) and the package registry.

Details

Registry name

io.github.cafferychen777/chatspatial

Version

1.6.0

Auth

No auth

Packages

pypi chatspatial

License

MIT

Repository

github.com/cafferychen777/ChatSpatial

Website

docs.cafferyang.com/

First seen

Oct 24, 2026

Last checked

Nov 1, 2026

Source

Official MCP Registrygithub-graphql