# encode-query-nexus

> encode-query-nexus — cici566-encode-query-nexus. Use this tool when you need to search, download, and analyze ENCODE functional genomics data experiments, providing a centralized nexus for querying and managing large datasets. It solves problems related to data discovery, access, and analysis for researchers and scientists. With git capabilities, it accepts queries and experiment IDs as inputs and outputs downloadable datasets and analysis results.

Canonical page: https://skillsregistry.net/skills/cici566-encode-query-nexus  
JSON: https://api.skillsregistry.net/v1/skills/cici566-encode-query-nexus

## Description

Best MCP Server for ENCODE Functional Genomics Data 2026 – Search, Download & Analyze Experiments

## Trust

- **Trust score (0–1):** 0.30
- **Verification tier:** unverified
- **Last scanned:** 2026-09-03

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** container
- **Runtime environment:** vm
- **Category:** search
- **Updated:** 2026-09-21

## Source

- **Source listing:** [GitHub](https://github.com/cici566/encode-query-nexus)

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "cici566-encode-query-nexus"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/cici566-encode-query-nexus` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/cici566-encode-query-nexus/pull`

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SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt