filter_genes.json

{
  "tool_id": "filter_genes",
  "name": "Gene Filtering",
  "category": "qc",
  "framework": "scanpy",
  "function": "sc.pp.filter_genes",
  "valid_after": [
    "qc"
  ],
  "valid_before": [
    "normalization"
  ],
  "paradigms": [
    "all"
  ],
  "parameters": {
    "min_cells": {
      "type": "int",
      "default": 3,
      "range": [
        1,
        10
      ],
      "guidance": "Minimum number of cells a gene must be expressed in to be retained. 3 is the standard default. Lower values keep more rare transcripts but increase noise."
    }
  },
  "outputs": {
    "filtered_adata": "AnnData with rarely-expressed genes removed",
    "genes_before": "int",
    "genes_after": "int"
  },
  "validation": {
    "min_retention_pct": 50,
    "check": "At least 50% of genes retained."
  },
  "provenance_captures": [
    "min_cells",
    "genes_before",
    "genes_after"
  ]
}