{"repo":"ammawla/encode-toolkit","free":true,"listed":false,"github":"https://github.com/ammawla/encode-toolkit","clone":"git clone https://github.com/ammawla/encode-toolkit.git","description":"MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments","language":"Python","stars":26,"topics":["ai","ai-agents","ai-bio","bioinformatics","bioinformatics-tool","claude","claude-code","claude-code-mcp","claude-code-plugin","claude-code-skills"],"license":"AGPL-3.0","category":"ai-agents","readme_excerpt":"ENCODE Toolkit — Genomics Research Infrastructure for Claude Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready methods — all from natural language in Claude Code. Start from ENCODE but go everywhere: discover histone peaks, cross-reference with GWAS variants, check ClinVar pathogenicity, pull GTEx expression, analyze TF binding motifs from JASPAR, run pipelines, and generate publication-ready methods with full provenance — in one conversation. --- Citation Notes If you use ENCODE-Toolkit , please cite: Alex M. Mawla. (2026). ENCODE-Toolkit: an MCP server, Claude plugin, and skills suite for ENCODE genomic data access and analysis . Zenodo. https://doi.org/10.5281/zenodo.18917511 BibTeX --- Quick Start Claude Code Plugin (recommended) Start a new Claude Code session and enter: That's it. All 20 tools, 47 skills, and the MCP connector are now available. MCP-only install (tools only, no skills) If you only need the 20 MCP tools without the 47 workflow skills: Other editors and platforms npx (Node.js) Or in MCP client config: { \"command\": \"npx\", \"args\": [\"encode-toolkit\"] } pip install Then use encode-toolkit as the command in any MCP client configuration: Claude Desktop (MCP only) Add to your claude desktop config.json : macOS : /Library/Application Support/Claude/claude desktop config.json Windows : %APPDATA%\\Claude\\claude desktop config.json No installation needed when using uvx . Just add the config and restart Claude. VS Co","default_branch":null,"files":null,"tree":[],"storefront":"/r/ammawla","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/ammawla/encode-toolkit/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}