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		Dr. Alex M. Mawla, PhD
		Email: ammawla@ucdavis.edu
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+2

-2

package.json

		{
		"name": "encode-toolkit",
		"version": "0.3.0-beta.10",
		"version": "0.3.0",
		"mcpName": "io.github.ammawla/encode-toolkit",
		@@ -26,3 +26,3 @@ "description": "ENCODE Toolkit — Genomics research infrastructure with 20 MCP tools, 47 skills, 14 database integrations, and 7 pipelines for Claude Code",
		"author": "Dr. Alex M. Mawla, PhD <ammawla@ucdavis.edu>",
		"license": "CC-BY-NC-4.0",
		"license": "AGPL-3.0-only",
		"repository": {
		@@ -29,0 +29,0 @@ "type": "git",

+29

-7

README.md

		@@ -5,5 +5,5 @@ # ENCODE Toolkit — Genomics Research Infrastructure for Claude

		[![License: CC BY-NC 4.0](https://img.shields.io/badge/License-CC_BY--NC_4.0-green.svg)](LICENSE)
		[![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-0.3.0--beta.10-yellow)](CHANGELOG.md)
		[![Version](https://img.shields.io/badge/version-0.3.0-green)](CHANGELOG.md)
		[![Status](https://img.shields.io/badge/status-beta-yellow)]()
		@@ -13,4 +13,4 @@ [![Skills](https://img.shields.io/badge/skills-47-orange)](docs/skill-vignettes/)
		[![Pipelines](https://img.shields.io/badge/pipelines-7-green)](skills/pipeline-chipseq/)
		[![Databases](https://img.shields.io/badge/databases-14-teal)](docs/SHOWCASE.md)
		[![Tests](https://img.shields.io/badge/tests-506_passing-brightgreen)](tests/)
		[![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/)
		@@ -20,2 +20,3 @@ [![Security](https://img.shields.io/badge/security-no_telemetry-blue)]()
		[![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/)
		@@ -25,4 +26,4 @@ [![PyPI Downloads](https://img.shields.io/pypi/dw/encode-toolkit?style=flat&label=PyPI%20Downloads)](https://pypi.org/project/encode-toolkit/)
		[![NPM Downloads](https://img.shields.io/npm/dw/encode-toolkit?style=flat&label=NPM%20Downloads)](https://www.npmjs.com/package/encode-toolkit)
		[![smithery badge](https://smithery.ai/badge/encode-toolkit)](https://smithery.ai/server/encode-toolkit)
		[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18917519.svg)](https://doi.org/10.5281/zenodo.18917519)
		[![GitHub Clones](https://img.shields.io/badge/dynamic/json?color=success&label=Clones&query=count&url=https://gist.githubusercontent.com/ammawla/8fdeb4cd92776739d329df9afd942b2e/raw/clone.json&logo=github)](https://github.com/ammawla/encode-toolkit)<br>
		[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18917519.svg)](https://doi.org/10.5281/zenodo.18917511)

		@@ -39,2 +40,23 @@ <a href="https://glama.ai/mcp/servers/ammawla/encode-toolkit">

		## 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

		```bibtex
		@software{mawla_2026_encode_toolkit,
		author = {Mawla, Alex M.},
		title = {ENCODE-Toolkit: an MCP server, Claude plugin, and skills suite for ENCODE genomic data access and analysis},
		year = {2026},
		publisher = {Zenodo},
		doi = {10.5281/zenodo.18917511},
		url = {https://doi.org/10.5281/zenodo.18917511}
		}
		```

		---

		## Quick Start
		@@ -791,4 +813,4 @@

		Restrictive Non-Commercial License. Free for personal, educational, and academic research. No derivative works without written permission. Commercial use requires a separate license. See [LICENSE](LICENSE) for full terms.
		AGPL-3.0. See [LICENSE](LICENSE) for full terms.

		For commercial licensing inquiries: ammawla@ucdavis.edu

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