encode-database

encode-database is a skill for Claude Code, Codex from jaechang-hits/SciAgent-Skills. It costs 124 tokens per session (8,945 once invoked), scanned A, original, no licence file.

A connection to the ENCODE Portal, a research database of gene-regulation experiments across many cell types. It provides regulatory genomics data such as protein-binding, open-chromatin, histone-mark, and RNA activity measurements.

In plain words
What is it for?
Use it to find experiments by assay, cell sample, or target; download BED and bigWig data; and retrieve candidate regulatory regions near genes or genomic regions.
Why use it?
It avoids manually searching ENCODE and downloading files when studying how DNA regions may affect gene activity.

Skill for Claude CodeCodex

Part of the sciagent-skills plugin — 56 skills shipped together

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.

agentmods
npx agentmods add skills/jaechang-hits/sciagent-skills/encode-database
Any agent
npx skills add jaechang-hits/SciAgent-Skills --skill encode-database
Clone the repo
git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills

Made for: Claude Code, Codex.

Or install sciagent-skills, the plugin that ships this one along with the rest of its 56 skills.

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-database

README.md
[![agentmods](https://agentmods.dev/badge/skills/jaechang-hits/sciagent-skills/encode-database.svg)](https://agentmods.dev/skills/jaechang-hits/sciagent-skills/encode-database)
Your own site
<a href="https://agentmods.dev/skills/jaechang-hits/sciagent-skills/encode-database"><img src="https://agentmods.dev/badge/skills/jaechang-hits/sciagent-skills/encode-database.svg" alt="Measured on agentmods" height="20"></a>
Per session 124 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 8,945 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 1 finding. Scan, not verified.
Origin unknown No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5 $0.00124 $0.08945
Opus 5 $0.00062 $0.04473
Sonnet 5 $0.00025 $0.01789
Haiku 4.5 $0.00012 $0.00894

Measured 4d ago against content hash 21de5a98ef92, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

encode-database scanned grade A with 1 finding 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 4d 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.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

r = requests.get(f"{BASE}/search/", params=params, timeout=30)
skills/genomics-bioinformatics/databases/encode-database/SKILL.md · 804 lines

The source is not reproduced here

No licence file

A repository with no LICENSE is all rights reserved by default, so the body is not copied here. The metadata, the measurements and the link are.

Read it on GitHub

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. 4d ago First seen · 804 lines · 124 tokens per session scan A 21de5a98ef92

Subscribe to this mod's changes

encode-database is a skill published in the GitHub repository jaechang-hits/SciAgent-Skills (359 stars, last pushed 6d ago), with no licence file. It adds 124 tokens to every session and 8,945 once invoked, about $0.0006 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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