Tangram Tools

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

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

Available Tools

run_tangram_deconvolution (Type: RemoteTool)

Deconvolve a spatial-transcriptomics assay into per-spot cell-type proportions using Tangram (Bia…

run_tangram_deconvolution tool specification

Tool Information:

  • Name: run_tangram_deconvolution

  • Type: RemoteTool

  • Description: Deconvolve a spatial-transcriptomics assay into per-spot cell-type proportions using Tangram (Biancalani 2021). Maps cell-type clusters from a single-cell reference AnnData onto a spatial AnnData (clusters mode, rna_count_based density prior) and projects the cell-type annotations to space, returning each spot’s cell-type composition and the dataset-wide mean proportions. Inputs are server-accessible .h5ad files; the single-cell reference obs must contain the cluster_label column.

Parameters:

  • sc_path (string) (required) Server-accessible path or URL to an .h5ad single-cell REFERENCE AnnData; obs must contain cluster_label.

  • sp_path (string) (required) Server-accessible path or URL to an .h5ad SPATIAL AnnData (spots x genes) to deconvolve.

  • cluster_label (string) (required) obs column in the single-cell reference naming the cell type/cluster (e.g. ‘cell_type’).

  • num_epochs (integer) (optional) Tangram mapping epochs (default 500).

Example Usage:

query = {
    "name": "run_tangram_deconvolution",
    "arguments": {
        "sc_path": "example_value",
        "sp_path": "example_value",
        "cluster_label": "example_value"
    }
}
result = tu.run(query)