Decoupler Ulm Tools

Configuration File: decoupler_ulm_tools.json Tool Type: Local Tools Count: 1

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

Available Tools

Activity_infer_ulm (Type: DecouplerULMTool)

Infer transcription-factor / pathway activities from a per-gene statistic (e.g. a DESeq2/edgeR t-…

Activity_infer_ulm tool specification

Tool Information:

  • Name: Activity_infer_ulm

  • Type: DecouplerULMTool

  • Description: Infer transcription-factor / pathway activities from a per-gene statistic (e.g. a DESeq2/edgeR t-stat or logFC) and a regulatory network (source=TF/pathway, target=gene, weight=mode of regulation), using decoupleR’s univariate-linear-model (ULM) method. Returns per-source activity (slope t-value; +=active) and p-value. Pure-compute; pairs with the DoRothEA/PROGENy networks from OmniPath_get_dorothea_regulon.

Parameters:

  • gene_stats ([‘object’, ‘null’]) (optional) {gene: statistic} mapping (e.g. DE t-statistic per gene). Alternative to genes+stats.

  • genes ([‘array’, ‘null’]) (optional) Gene identifiers (use with stats, same order).

  • stats ([‘array’, ‘null’]) (optional) Per-gene statistic (same order as genes).

  • network (array) (required) Regulatory edges: [{source, target, weight}] (weight defaults to 1; ‘mor’ accepted as an alias).

  • min_targets ([‘integer’, ‘null’]) (optional) Minimum targets present in the gene list for a source to be tested (default 5).

Example Usage:

query = {
    "name": "Activity_infer_ulm",
    "arguments": {
        "network": ["item1", "item2"]
    }
}
result = tu.run(query)