encode-toolkit
byammawla· 1 MCP server
MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments
How to install encode-toolkit?
ammawla/encode-toolkit
$git clone https://github.com/ammawla/encode-toolkitInstalls into the current project.
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Install encode-toolkit by running `git clone https://github.com/ammawla/encode-toolkit`, then use it for the current task and follow its documentation at https://github.com/ammawla/encode-toolkit.
README.md
| 1 | # ENCODE Toolkit — Genomics Research Infrastructure for Claude |
| 2 | |
| 3 | <!-- mcp-name: io.github.ammawla/encode-toolkit --> |
| 4 | |
| 5 | [](LICENSE) |
| 6 | [](https://www.python.org/downloads/) |
| 7 | [](CHANGELOG.md) |
| 8 | []() |
| 9 | [](docs/skill-vignettes/) |
| 10 | [](src/encode_connector/server/main.py) |
| 11 | [](skills/pipeline-chipseq/) |
| 12 | [](docs/SHOWCASE.md)<br> |
| 13 | [](tests/) |
| 14 | [](tests/) |
| 15 | []() |
| 16 | [](https://claude.com/claude-code) |
| 17 | []() |
| 18 | [](https://smithery.ai/server/encode-toolkit) <br> |
| 19 | [](https://pypi.org/project/encode-toolkit/) |
| 20 | [](https://pypi.org/project/encode-toolkit/) |
| 21 | [](https://www.npmjs.com/package/encode-toolkit) |
| 22 | [](https://www.npmjs.com/package/encode-toolkit) |
| 23 | [](https://github.com/ammawla/encode-toolkit)<br> |
| 24 | [](https://doi.org/10.5281/zenodo.18917511) |
| 25 | |
| 26 | <a href="https://glama.ai/mcp/servers/ammawla/encode-toolkit"> |
| 27 | <img width="380" height="200" src="https://glama.ai/mcp/servers/ammawla/encode-toolkit/badge" /> |
| 28 | </a> |
| 29 | |
| 30 | Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready methods — all from natural language in Claude Code. |
| 31 | |
| 32 | > 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. |
| 33 | |
| 34 | --- |
| 35 | |
| 36 | ## Citation Notes |
| 37 | |
| 38 | If you use **ENCODE-Toolkit**, please cite: |
| 39 | |
| 40 | 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 |
| 41 | |
| 42 | ### BibTeX |
| 43 | |
| 44 | ```bibtex |
| 45 | @software{mawla_2026_encode_toolkit, |
| 46 | author = {Mawla, Alex M.}, |
| 47 | title = {ENCODE-Toolkit: an MCP server, Claude plugin, and skills suite for ENCODE genomic data access and analysis}, |
| 48 | year = {2026}, |
| 49 | publisher = {Zenodo}, |
| 50 | doi = {10.5281/zenodo.18917511}, |
| 51 | url = {https://doi.org/10.5281/zenodo.18917511} |
| 52 | } |
| 53 | ``` |
| 54 | |
| 55 | --- |
| 56 | |
| 57 | ## Quick Start |
| 58 | |
| 59 | ### Claude Code Plugin (recommended) |
| 60 | |
| 61 | Start a new Claude Code session and enter: |
| 62 | |
| 63 | ``` |
| 64 | /plugin marketplace add ammawla/encode-toolkit |
| 65 | |
| 66 | /plugin install encode-toolkit |
| 67 | ``` |
| 68 | |
| 69 | That's it. All 20 tools, 47 skills, and the MCP connector are now available. |
| 70 | |
| 71 | <details> |
| 72 | <summary><strong>MCP-only install (tools only, no skills)</strong></summary> |
| 73 | |
| 74 | If you only need the 20 MCP tools without the 47 workflow skills: |
| 75 | |
| 76 | ```bash |
| 77 | claude mcp add encode -- uvx encode-toolkit |
| 78 | ``` |
| 79 | |
| 80 | </details> |
| 81 | |
| 82 | <details> |
| 83 | <summary><strong>Other editors and platforms</strong></summary> |
| 84 | |
| 85 | #### npx (Node.js) |
| 86 | |
| 87 | ```bash |
| 88 | npx encode-toolkit |
| 89 | ``` |
| 90 | |
| 91 | Or in MCP client config: `{ "command": "npx", "args": ["encode-toolkit"] }` |
| 92 | |
| 93 | #### pip install |
| 94 | |
| 95 | ```bash |
| 96 | pip install encode-toolkit |
| 97 | ``` |
| 98 | |
| 99 | Then use `encode-toolkit` as the command in any MCP client configuration: |
| 100 | |
| 101 | ```json |
| 102 | { |
| 103 | "mcpServers": { |
| 104 | "encode": { |
| 105 | "command": "encode-toolkit" |
| 106 | } |
| 107 | } |
| 108 | } |
| 109 | ``` |
| 110 | |
| 111 | </details> |
| 112 | |
| 113 | <details> |
| 114 | <summary><strong>Claude Desktop (MCP only)</strong></summary> |
| 115 | |
| 116 | Add to your `claude_desktop_config.json`: |
| 117 | |
| 118 | **macOS**: `~/Library/Application Support/Claude/claude_desktop_config.json` |
| 119 | **Windows**: `%APPDATA%\Claude\claude_desktop_config.json` |
| 120 | |
| 121 | ```json |
| 122 | { |
| 123 | "mcpServers": { |
| 124 | "encode": { |
| 125 | "command": "uvx", |
| 126 | "args": ["encode-toolkit"] |
| 127 | } |
| 128 | } |
| 129 | } |
| 130 | ``` |
| 131 | |
| 132 | > No installation needed when using `uvx`. Just add the config and restart Claude. |
| 133 | |
| 134 | </details> |
| 135 | |
| 136 | <details> |
| 137 | <summary><strong>VS Code / Copilot</strong></summary> |
| 138 | |
| 139 | Add to `.vscode/mcp.json` in your workspace: |
| 140 | |
| 141 | ```json |
| 142 | { |
| 143 | "mcp": { |
| 144 | "servers": { |
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