Squidpy Tools

Configuration File: remote_tools/squidpy_tools.json Tool Type: Remote Tools Count: 1

This page contains all tools defined in the squidpy_tools.json configuration file.

Available Tools

run_squidpy_nhood_enrichment (Type: RemoteTool)

Run Squidpy (Palla et al., Nature Methods 2022) neighborhood enrichment on spatial single-cell da…

run_squidpy_nhood_enrichment tool specification

Tool Information:

  • Name: run_squidpy_nhood_enrichment

  • Type: RemoteTool

  • Description: Run Squidpy (Palla et al., Nature Methods 2022) neighborhood enrichment on spatial single-cell data. Builds a spatial neighbors graph from cell coordinates in adata.obsm[‘spatial’], then permutation-tests which pairs of cluster categories (e.g. cell types) are co-localized (enriched, positive z-score) or segregated (depleted, negative z-score). Returns the category x category z-score matrix plus the category labels. Input is a server-accessible spatial .h5ad with adata.obsm[‘spatial’] coordinates and cluster_key in adata.obs.

Parameters:

  • adata_path (string) (required) Server-accessible path or URL to a spatial .h5ad AnnData with adata.obsm[‘spatial’] coordinates and cluster_key in adata.obs.

  • cluster_key (string) (required) obs column with the categorical cluster/cell-type labels to test for co-localization (e.g. ‘cell_type’).

  • n_neighs (integer) (optional) Number of nearest spatial neighbors per cell when building the graph (default 6).

Example Usage:

query = {
    "name": "run_squidpy_nhood_enrichment",
    "arguments": {
        "adata_path": "example_value",
        "cluster_key": "example_value"
    }
}
result = tu.run(query)