Encode Toolkit
by ammawlacommunityv0.3.0-beta.5
7
5
ENCODE Toolkit is a genomics research infrastructure that allows users to search ENCODE data, cross-reference multiple databases, run analysis pipelines, and generate publication-ready methods using natural language queries.
From the registry: 20 MCP tools + 48 skills for ENCODE Project genomics — search, download, pipelines
Install & configure
Prerequisites
- required
Install in your client
Paste into the AI you're chatting with — it will figure out the rest
Please install the `encode-toolkit` MCP server into my current AI client (that's you).
Required prerequisites (do these first if not already done):
- **Install uv/uvx** — Requires uv (uvx) to run the PyPI package. Run: `pip install uv` (https://docs.astral.sh/uv/)
Canonical MCP server config (stdio transport):
- command: `uvx`
- args: ["encode-toolkit"]
Note: ENCODE genomics toolkit. 20 MCP tools, 47 skills when installed as Claude Code plugin. Most ENCODE data is public; no credentials required by default. Can also be installed via npx encode-toolkit or pip install encode-toolkit.
Add this MCP server to my current client's config in the correct format for you. If you need secrets or credentials I haven't provided, ASK me — do not invent values or leave raw placeholders. After adding it, tell me how to verify the server is connected.Note: ENCODE genomics toolkit. 20 MCP tools, 47 skills when installed as Claude Code plugin. Most ENCODE data is public; no credentials required by default. Can also be installed via npx encode-toolkit or pip install encode-toolkit.
Tools (5)
encode_search_experiments
Search ENCODE experiments with various filters.
encode_get_experiment
Get full details for a single experiment including all files and metrics.
encode_download_files
Download specific files by accession to a local directory.
encode_batch_download
Search and download files in one step.
encode_track_experiment
Track an experiment locally with its publications and methods.
Prerequisites
- • Python 3.10+
Packages
encode-toolkit
npmv0.3.0-beta.5transport: stdio
encode-toolkit
pypiv0.3.0b5transport: stdio
Details
- Language
- Python
- License
- AGPL-3.0
- Released
- Mar 9, 2026
- Last commit
- Apr 19, 2026
- Registry name
- io.github.ammawla/encode-toolkit