`differential-expression`POST

Run RNA-seq differential gene expression analysis with DESeq2, edgeR, and limma-voom.

Runs differential gene expression analysis from a raw count matrix and sample metadata. Supports DESeq2, edgeR, limma-voom, or all three methods, returning structured DEG tables, method summaries, consensus genes, QC metrics, and warnings.

Endpoint

POST https://api.frontwind.ai/v1/agents/differential-expression

Example

curl -X POST https://api.frontwind.ai/v1/agents/differential-expression \
  -H "Authorization: Bearer fw_live_..." \
  -H "Content-Type: application/json" \
  -d '{ "counts_csv": "gene_id,ctrl_1,ctrl_2,trt_1,trt_2\\nGeneA,10,12,80,90\\n", "metadata_csv": "sample_id,condition\\nctrl_1,control\\nctrl_2,control\\ntrt_1,treated\\ntrt_2,treated\\n", "condition_column": "condition", "reference_group": "control", "comparison_group": "treated", "method": "all" }'

Request body

Field	Type	Required	Description
`count_file_id`	`string`	No	Website upload file ID for the count matrix. Use counts_csv for direct API calls.
`metadata_file_id`	`string`	No	Website upload file ID for sample metadata. Use metadata_csv for direct API calls.
`counts_csv`	`string`	No	Inline CSV/TSV count matrix.
`metadata_csv`	`string`	No	Inline CSV/TSV sample metadata.
`gene_id_column`	`string`	No
`sample_id_column`	`string`	No
`condition_column`	`string`	Yes
`reference_group`	`string`	Yes
`comparison_group`	`string`	Yes
`method`	`string`	default "all"
`min_count`	`integer`	default 10
`fdr_cutoff`	`number`	default 0.05
`log2fc_cutoff`	`number`	default 1
`use_cache`	`boolean`	default false

Response data

Field	Type	Description
`summary`	`object`
`sample_qc`	`object`
`method_results`	`array`
`consensus`	`object`
`warnings`	`array`

Example response

{
  "ok": true,
  "agent": "differential-expression",
  "data": {
    "summary": {
      "comparison": "treated vs control",
      "methods_completed": [
        "DESeq2",
        "edgeR",
        "limma-voom"
      ],
      "significant_by_method": {
        "DESeq2": 42,
        "edgeR": 38,
        "limma-voom": 35
      }
    },
    "method_results": [
      {
        "method": "DESeq2",
        "n_tested": 18000,
        "n_significant": 42,
        "top_up": [
          {
            "gene_id": "GeneA",
            "log2FC": 2.8,
            "padj": 0.001
          }
        ]
      }
    ],
    "consensus": {
      "n_methods": 3,
      "n_consensus_significant": 20,
      "genes": [
        "GeneA"
      ]
    },
    "warnings": []
  },
  "elapsed_s": 42
}