cluster_profiler.json

{
  "tool_id": "cluster_profiler",
  "name": "clusterProfiler GO/KEGG Enrichment",
  "category": "enrichment",
  "framework": "clusterProfiler",
  "function": "clusterProfiler::enrichGO / enrichKEGG (R via subprocess)",
  "valid_after": ["differential_expression"],
  "valid_before": [],
  "paradigms": ["all"],
  "parameters": {
    "organism": {
      "type": "string",
      "default": "org.Hs.eg.db",
      "options": ["org.Hs.eg.db", "org.Mm.eg.db"],
      "guidance": "Annotation database. 'org.Hs.eg.db' for human, 'org.Mm.eg.db' for mouse."
    },
    "ont": {
      "type": "string",
      "default": "BP",
      "options": ["BP", "MF", "CC", "ALL"],
      "guidance": "GO ontology: BP (Biological Process, most common), MF (Molecular Function), CC (Cellular Component), ALL."
    },
    "pvalue_cutoff": {
      "type": "float",
      "default": 0.05
    },
    "qvalue_cutoff": {
      "type": "float",
      "default": 0.1
    },
    "min_gs_size": {
      "type": "int",
      "default": 10,
      "guidance": "Minimum gene set size."
    },
    "max_gs_size": {
      "type": "int",
      "default": 500,
      "guidance": "Maximum gene set size."
    }
  },
  "outputs": {
    "enrichment_results": "DataFrame with Description, GeneRatio, pvalue, p.adjust, qvalue, geneID"
  },
  "validation": {
    "check": "Results should contain significant terms. Check for redundancy — use simplify() to reduce redundant GO terms."
  },
  "provenance_captures": ["organism", "ont", "pvalue_cutoff", "qvalue_cutoff", "n_genes_input", "n_terms_significant"]
}