vibed-lab / plugins

ammawla/encode-toolkit

21 stars · Last commit 2026-09-27

MCP server and Claude Code plugin for the ENCODE Project: search, download and analyze ChIP-seq, ATAC-seq, RNA-seq, WGBS, Hi-C and CUT&RUN data with 20 tools, 47 skills and 7 Nextflow pipelines

PluginWorkflow & AutomationTDD & TestingDocumentationDevOps & InfraAI & PromptingData & MLSecurity

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# ENCODE Toolkit — Genomics Research Infrastructure for Claude

<!-- mcp-name: io.github.ammawla/encode-toolkit -->

[![License: AGPL-3.0](https://img.shields.io/badge/license-AGPL--3.0-green.svg)](LICENSE)
[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
[![Version](https://img.shields.io/badge/version-0.3.4-green)](CHANGELOG.md)
[![Status](https://img.shields.io/badge/status-beta-yellow)]()
[![Skills](https://img.shields.io/badge/skills-47-orange)](docs/skill-vignettes/)
[![Tools](https://img.shields.io/badge/MCP_tools-20-purple)](src/encode_connector/server/main.py)
[![Pipelines](https://img.shields.io/badge/pipelines-7-green)](skills/pipeline-chipseq/)
[![Databases](https://img.shields.io/badge/databases-14-teal)](docs/SHOWCASE.md)<br>
[![Tests](https://img.shields.io/badge/tests-568_passing-brightgreen)](tests/)
[![Coverage](https://img.shields.io/badge/coverage-98%25-brightgreen)](tests/)
[![Security](https://img.shields.io/badge/security-no_telemetry-blue)]()
[![Claude Code](https://img.shields.io/badge/Claude_Code-plugin-blueviolet)](https://claude.com/claude-code)
[![Provenance](https://img.shields.io/badge/provenance-full_audit_trail-green)]()
[![smithery badge](https://smithery.ai/badge/encode-toolkit)](https://smithery.ai/server/encode-toolkit) <br>
[![PyPI version](https://img.shields.io/pypi/v/encode-toolkit.svg?include_prereleases)](https://pypi.org/project/encode-toolkit/)
[![PyPI Downloads](https://img.shields.io/pypi/dw/encode-toolkit?style=flat&label=PyPI%20Downloads)](https://pypi.org/project/encode-toolkit/)

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