Paga Tools

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

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

Available Tools

run_paga_trajectory (Type: RemoteTool)

Run PAGA (Partition-based Graph Abstraction; Wolf et al., Genome Biology 2019) on a single-cell A…

run_paga_trajectory tool specification

Tool Information:

  • Name: run_paga_trajectory

  • Type: RemoteTool

  • Description: Run PAGA (Partition-based Graph Abstraction; Wolf et al., Genome Biology 2019) on a single-cell AnnData to estimate connectivity between cell clusters and sketch the trajectory backbone. Builds a neighbors graph if one is absent (log-normalize -> PCA -> neighbors), runs scanpy.tl.paga, then returns the cluster x cluster connectivity matrix plus the strongest connected cluster pairs (edges above a threshold). Input is a server-accessible .h5ad whose obs contains the requested cluster_key.

Parameters:

  • adata_path (string) (required) Server-accessible path or URL to an .h5ad AnnData whose obs contains cluster_key.

  • cluster_key (string) (required) obs column holding the discrete cluster labels (e.g. ‘leiden’ or ‘cell_type’).

  • threshold (number) (optional) Minimum connectivity for an edge to be reported (default 0.1).

Example Usage:

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