Ssgsea Tools

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

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

Available Tools

ssGSEA_score (Type: SSGSEATool)

Single-sample GSEA (Barbie 2009): score each sample for each gene set from an expression matrix (…

ssGSEA_score tool specification

Tool Information:

  • Name: ssGSEA_score

  • Type: SSGSEATool

  • Description: Single-sample GSEA (Barbie 2009): score each sample for each gene set from an expression matrix (genes x samples), producing a gene_set x sample signature-score matrix. Positive = the set’s genes are among that sample’s highly-expressed genes. Basis for per-sample signature scoring (immune infiltration, pathway activity). Pure-compute (no R); supply gene sets from MSigDB/Enrichr.

Parameters:

  • expression (object) (required) {gene: [value_per_sample, …]} — a genes x samples expression matrix (e.g. log-normalized).

  • samples ([‘array’, ‘null’]) (optional) Sample names (same order as the per-gene value lists); defaults to sample_1..

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

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

  • alpha ([‘number’, ‘null’]) (optional) Rank-weighting exponent (default 0.25, the ssGSEA standard).

Example Usage:

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