Gsea Prerank Tools

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

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

Available Tools

GSEA_prerank (Type: GSEAPrerankTool)

Pre-ranked Gene Set Enrichment Analysis (Subramanian 2005) on a ranked gene list (e.g. genes rank…

GSEA_prerank tool specification

Tool Information:

  • Name: GSEA_prerank

  • Type: GSEAPrerankTool

  • Description: Pre-ranked Gene Set Enrichment Analysis (Subramanian 2005) on a ranked gene list (e.g. genes ranked by a DESeq2/edgeR statistic) against one or more gene sets. Returns per-set enrichment score (ES), normalized ES (NES), permutation p-value, and leading-edge genes. Pure-compute (no R, no bundled MSigDB - supply gene sets, e.g. from Enrichr). Complements over-representation tools by using the full ranking.

Parameters:

  • ranked_genes ([‘object’, ‘null’]) (optional) {gene: score} mapping (score = DE statistic / fold change). Genes are ranked by score descending. Alternative to genes+scores.

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

  • scores ([‘array’, ‘null’]) (optional) Per-gene ranking metric (same order as genes).

  • gene_sets ([‘object’, ‘null’]) (optional) {set_name: [gene, …]} collection to test. Alternative to gene_set.

  • gene_set ([‘array’, ‘null’]) (optional) A single gene set (list of gene symbols).

  • weight ([‘number’, ‘null’]) (optional) Score weighting exponent for the running sum (default 1.0; classic GSEA).

  • n_permutations ([‘integer’, ‘null’]) (optional) Gene-label permutations for the p-value (default 1000).

Example Usage:

query = {
    "name": "GSEA_prerank",
    "arguments": {
    }
}
result = tu.run(query)