agentmods.dev

encode-toolkit

encode-toolkit is a plugin for Claude Code from ammawla/encode-toolkit. Its manifest loads nothing; the 47 skills, 1 MCP server it bundles cost 4,665 tokens per session together, scanned A, original, AGPL-3.0.

A research toolkit for working with ENCODE, a public genomics project that catalogs how genes are regulated. It provides API tools and expert guidance for searching experiments, downloading data, running analysis pipelines, and comparing results across 14 databases.

In plain words
What is it for?
Use it to find ENCODE experiments, retrieve and verify genomics files, run analysis pipelines, and cross-reference biological data across databases.
Why use it?
It removes the need to build separate connections to research databases and manually check downloaded files. MD5 checks verify that downloaded files match the originals.

Plugin for Claude Code

Written for Claude Code: a Claude Code plugin manifest.

not rated 21repo changed 1mo ago A scan tokens not measured AGPL-3.0

Good fit Use it to find ENCODE experiments, retrieve and verify genomics files, run analysis pipelines, and cross-reference biological data across databases.

Compare 6 plugins from other repositories ↓
Install in Claude Code
/plugin marketplace add ammawla/encode-toolkit
/plugin install encode-toolkit
View source ↗ ammawla/encode-toolkit pypi.org
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Clone the repo
git clone --depth 1 https://github.com/ammawla/encode-toolkit

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for encode-toolkit

README.md
[![agentmods](https://agentmods.dev/badge/plugins/ammawla/encode-toolkit/plugin/github.svg)](https://agentmods.dev/plugins/ammawla/encode-toolkit/plugin)
Your own site
<a href="https://agentmods.dev/plugins/ammawla/encode-toolkit/plugin"><img src="https://agentmods.dev/badge/plugins/ammawla/encode-toolkit/plugin/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for encode-toolkit

Your own site · 80×15
<a href="https://agentmods.dev/plugins/ammawla/encode-toolkit/plugin"><img src="https://agentmods.dev/badge/plugins/ammawla/encode-toolkit/plugin.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session not measured What this adds to a session before it is invoked.
When invoked not measured The manifest loads nothing itself; its 47 skills, 1 MCP server cost 4,665 tokens a session between them.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Security

Grade A, and why

encode-toolkit scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

plugin/.claude-plugin/plugin.json · 22 lines

The source is not reproduced here

Licensed AGPL-3.0

The repository is licensed AGPL-3.0, which this catalogue does not treat as permission to reproduce the file. Read it at the source.

Read it on GitHub

Contents

What it installs

The manifest is a name and a version. 47 skills, 1 MCP server travel with it, and installing the plugin installs all of them — 4,665 tokens a session between them. Each is measured on its own page, and each can be installed alone.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 1mo ago Changed a3d37fd0be44
  2. 1mo ago Changed 59d1f1cc2d16
  3. 1mo ago First seen · 22 lines scan A aab365b8a759

Subscribe to this mod's changes

encode-toolkit is a plugin published in the GitHub repository ammawla/encode-toolkit (21 stars, last pushed 26d ago), licensed AGPL-3.0. Its token cost is not measured: this kind of file is read by the harness, not the model. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

ResearchScientificaiai-agentsai-biobioinformaticsbioinformatics-toolclaude
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