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ChatSpatial

Schema-enforced spatial transcriptomics analysis with 20 tools and 67 methods.

Connector by cafferychen777 · GitHub account verified by the MCP Registry

IndexedMITLocal (stdio)★ 45
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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

Asks which of your tools to add it to (Claude Code, Codex, Cursor, VS Code, Windsurf, Gemini CLI, Claude Desktop) and shows the change first. See https://agentmart.dev/cli.

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About

Schema-enforced spatial transcriptomics analysis with 20 tools and 67 methods via MCP

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Permissions

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
Secrets
None asked for
Install scripts
None found
Runs as
Python package

Tools by what they do 20

Read from the source code; the running server may list different tools.

Read 13 · Look things up without changing anything.

  • analyze_cell_communication
  • analyze_cnv
  • analyze_enrichment
  • analyze_spatial_statistics
  • analyze_trajectory_data
  • analyze_velocity_data
  • compare_conditions
  • compute_embeddings
  • find_markers
  • find_spatial_genes
  • identify_spatial_domains
  • integrate_samples
Show 1 more tools
  • visualize_data

Write 3 · Create, change, send or run things.

  • annotate_cell_types
  • preprocess_data
  • register_spatial_data

Not yet classified 4 · We could not tell from the name and description.

  • deconvolve_data
  • export_data
  • load_data
  • reload_data

Network hosts it talks to 15

  • ::1 · found in code
  • api.anthropic.com · found in code
  • cran.r-project.org · found in code
  • docs.cafferyang.com · found in code
  • doi.org · found in code
  • ensembl.org · found in code
  • ftp.ensembl.org · found in code
  • generativelanguage.googleapis.com · found in code
  • geodacenter.github.io · found in code
  • github.com · found in code
  • maayanlab.cloud · found in code
  • pysal.org · found in code
  • r-project.org · found in code
  • raw.githubusercontent.com · found in code
  • scvi-tools.org · found in code

Files it touches

  • /dev/null
  • /tmp/my_outputs
  • /Users/me/chatspatial/chatspatial
  • /Users/me/data
  • Your home directory (~)
  • ~/.chatspatial/results/my_data/differential_expression/wilcoxon_rank_genes_groups.csv
  • Any path the agent passes to its tools

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.

Show 5 more tools
  • load_data

    Load spatial transcriptomics data with comprehensive metadata profile. Args: data_path: Path to data file or directory data_type: 'visium', 'xenium', 'slide_seq', 'merfish', 'seqfish', or 'generic' name: Optional dataset name Returns: SpatialDataset with cell/gene counts and metadata profiles

  • preprocess_data

    Run QC, filtering, normalization, and highly variable gene selection. This tool does not compute PCA, UMAP, clustering, or neighbor graphs. Run compute_embeddings() afterward when downstream tools require those artifacts. Args: data_id: Dataset ID params: Preprocessing parameters (all have sensible defaults)

  • register_spatial_data

    Register/align spatial transcriptomics data across sections Args: source_id: Source dataset ID target_id: Target dataset ID to align to params: Registration parameters (method, alignment settings, etc.) Returns: Registration result with method, dataset IDs, spot counts, and registered spatial key

  • reload_data

    Reload dataset from disk after external script modifications. Args: data_id: Dataset ID to reload (must exist in MCP memory) path: Custom path (default: ~/.chatspatial/active/{data_id}.h5ad) Returns: Summary of reloaded dataset

  • visualize_data

    Visualize spatial transcriptomics data. Set plot_type and subtype in params; see VisualizationParameters schema for all options. Args: data_id: Dataset ID params: Visualization parameters (plot_type, subtype, genes, output_format, dpi, etc.)

Signals

Stars
45
Forks
14
Open issues
4
Weekly downloads
311
Last commit
Oct 20, 2026 (8 days ago)
Last release
Oct 20, 2026 (8 days ago)
Last package publish
Oct 20, 2026 (8 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
Oct 25, 2026
Source
Official MCP Registrygithub-graphql
Cite this page

ChatSpatial MCP server. Agent Mart. https://agentmart.dev/connectors/cafferychen777-chatspatial (last updated 2026-10-25)