Harmony Tools

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

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

Available Tools

run_harmony_integrate (Type: RemoteTool)

Integrate single-cell data across batches/samples with Harmony (Korsunsky et al., Nature Methods …

run_harmony_integrate tool specification

Tool Information:

  • Name: run_harmony_integrate

  • Type: RemoteTool

  • Description: Integrate single-cell data across batches/samples with Harmony (Korsunsky et al., Nature Methods 2019) — the default batch-correction baseline. Computes (or reuses an existing X_pca) a PCA embedding and returns the batch-corrected PCA embedding (X_pca_harmony), the standard input to neighbor graphs / clustering / UMAP. Harmony is fast and CPU-friendly even on large datasets. Input is a server-accessible .h5ad AnnData.

Parameters:

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

  • batch_key (string) (required) obs column naming the batch/sample to integrate over.

  • n_pcs (integer) (optional) Number of principal components to compute/use for Harmony (default 30).

Example Usage:

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