Scrublet Tools

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

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

Available Tools

run_scrublet_doublets (Type: RemoteTool)

Detect technical doublets in a single-cell RNA-seq count matrix with Scrublet (Wolock et al., Cel…

run_scrublet_doublets tool specification

Tool Information:

  • Name: run_scrublet_doublets

  • Type: RemoteTool

  • Description: Detect technical doublets in a single-cell RNA-seq count matrix with Scrublet (Wolock et al., Cell Systems 2019). Simulates synthetic doublets from observed transcriptomes and scores each real cell by its local density of simulated doublets, returning a per-cell doublet_score and a boolean predicted_doublet call — so doublets can be filtered before clustering/annotation. Input is a server-accessible .h5ad of RAW counts (not normalized/log data).

Parameters:

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

  • expected_doublet_rate (number) (optional) Expected fraction of transcriptomes that are doublets (default 0.06; scale ~0.008 per 1000 cells loaded for 10x).

Example Usage:

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