ENCODE Toolkit

A single-plugin Claude Code marketplace providing MCP tools and skills for working with the ENCODE Project functional-genomics data resource.

Unsigned

Overview

A Claude Code marketplace by Dr. Alex M. Mawla (UC Davis) bundling one content-dense plugin, encode-toolkit: 20 MCP tools plus 47 expert skills for the ENCODE (Encyclopedia of DNA Elements) Project, an NHGRI-funded functional-genomics data consortium. The plugin covers searching ENCODE experiments, downloading files with MD5 verification, running pipelines, and cross-referencing 14 ENCODE-related databases. Catalogued here under this registry's bundle admission test (internal project documentation Phase 10): not itself a GA4GH-sponsored project, but a real, publicly discoverable collection with a concrete genomics-research relevance fact -- ENCODE is a named, real, government-funded genomics data resource, the same class of fact as the registry's first bundle entry's Synapse.org link. Only one plugin is listed, but its scope (20 tools, 47 skills, one named external data resource) is substantive rather than a thin wrapper. Terms check: the repository carries a real root LICENSE file (GNU AGPLv3, confirmed by direct fetch), and the README states plainly "License: AGPL-3.0. See LICENSE for full terms", with no "or later" language found anywhere in the repository, so license is recorded as the SPDX-precise agpl-3.0-only identifier rather than the ambiguous bare AGPL-3.0 GitHub reports. None of its plugin names collide with this registry's own seeded plugin entries (all ga4gh-* slugs), so ga4gh.members is empty.

Details

Licence: AGPL-3.0-only
Version: 0.3.0
Category: genomics
Homepage: https://github.com/ammawla/encode-toolkit
Repository: https://github.com/ammawla/encode-toolkit
Maintainers: Susheel Varma (@susheel, GA4GH AI Workstream / Sage Bionetworks)
Keywords: genomicsencodefunctional-genomicsclaude-code-marketplace

Safety classification

No safety classification has been submitted for this entry.

Marketplace

Marketplace name: ammawla
Curated by: Dr. Alex M. Mawla, PhD
Plugins in this bundle: 1
Source: https://raw.githubusercontent.com/ammawla/encode-toolkit/main/.claude-plugin/marketplace.json

Bundled plugins

encode-toolkit — 20 ENCODE API tools + 47 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases.

This is a cached snapshot of the marketplace manifest at https://raw.githubusercontent.com/ammawla/encode-toolkit/main/.claude-plugin/marketplace.json, last synced at 2026-09-08T00:00:00.000Z. See the source for the authoritative, live listing.

Provenance

Created: 2026-09-08T00:00:00.000Z
Updated: 2026-09-08T00:00:00.000Z
Last verified: 2026-09-08T00:00:00.000Z