FourDN Search Data

Overview

Search 4DN Data Portal for Hi-C chromatin conformation files and experiments. Access 350+ uniformly processed Hi-C contact files from multiple technologies (in situ Hi-C, Capture Hi-C, Micro-C XL). Search by assay type, cell type, or keywords. Returns file metadata with download URLs. Note: Downloads require free 4DN account (create at data.4dnucleome.org). Use for: finding Hi-C datasets, discovering 3D genome data, accessing TAD (Topologically Associating Domain) boundaries, A/B compartments, chromatin loop calls.

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed

1d ago

Last success

1d ago

Last latency

125ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "assay_title": {
      "description": "Filter by assay (e.g., 'Hi-C', 'Micro-C', 'Capture Hi-C')",
      "type": "string"
    },
    "biosource_name": {
      "description": "Filter by cell type (e.g., 'H1-hESC', 'HFFc6', 'GM12878')",
      "type": "string"
    },
    "file_type": {
      "description": "Filter by file type. Common types: 'contact list' (processed contact matrices), 'pairs' (aligned read pairs), 'cooler' (multi-resolution contact matrices), 'mcool' (multi-resolution cooler), 'hic' (Juicer format).",
      "type": "string"
    },
    "item_type": {
      "default": "File",
      "description": "Type of item to search",
      "enum": [
        "File",
        "Experiment",
        "Biosource"
      ],
      "type": "string"
    },
    "limit": {
      "default": 25,
      "description": "Maximum results to return",
      "maximum": 100,
      "minimum": 1,
      "type": "integer"
    },
    "operation": {
      "default": "search",
      "enum": [
        "search"
      ],
      "type": "string"
    },
    "query": {
      "default": "*",
      "description": "Search query (default: '*' for all)",
      "type": "string"
    }
  },
  "required": [
    "operation"
  ],
  "type": "object"
}

Examples (1)

{
  "limit": 3,
  "operation": "",
  "query": "BRCA1"
}

Identifiers

Catalog ID

tu_FourDN_search_data

Tool name

FourDN_search_data

Added

2026-04-30 22:47Z

Tags

tooluniverse