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regulatory-elements SKILL.md skillA

This file is byte-identical to the first copy the registry indexed. Same content hash, so the same checks give both the same grade.

regulatory-elements from ammawla/encode-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.

Install it, pinned

mdr add ammawla/encode-toolkit/regulatory-elements@git:20260920.6050003

Pins git:20260920.6050003 in mdr.lock. Pin the fingerprint instead.

Audit grade: A, 17 of 17 checks passed
Kind: SKILL.md skill
Repository: ammawla/encode-toolkit
Path: skills/regulatory-elements/SKILL.md
Versions recorded: 3
Latest version: git:20260920.6050003, committed Sep 20, 2026
First version recorded: Mar 8, 2026
Size: 27,702 bytes
Repository stars: 21
License: AGPL-3.0

Discover and characterize regulatory elements (enhancers, promoters, silencers, insulators, super-enhancers) using ENCODE data and the cCRE catalog. Use when the user wants to find candidate regulatory elements, identify active enhancers in a tissue, map promoter states, classify chromatin states with ChromHMM, identify super-enhancers with ROSE, understand the functional validation hierarchy (CRISPR > MPRA > reporter), or characterize non-coding genomic regions. Covers the full workflow from…

Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.

What the file says

# Discover and Characterize Regulatory Elements with ENCODE

## When to Use

- User wants to find enhancers, promoters, silencers, or insulators in a specific tissue using ENCODE
- User asks about "regulatory elements", "cCREs", "enhancer discovery", "ChromHMM", or "super-enhancers"
- User needs to classify chromatin states or identify active regulatory regions from histone mark data
- User wants to use ENCODE's 926,535 cCRE catalog or run functional validation (CRISPR/MPRA/reporter)
- Example queries: "find active enhancers in liver", "classify chromatin states for my tissue", "identify super-enhancers from H3K27ac data"

Identify, classify, and functionally characterize regulatory elements using ENCODE's catalog of 926,535 human candidate cis-regulatory elements (cCREs) and layered functional genomics data.

## Scientific Rationale

**The question**: "What regulatory elements are active in my tissue of interest, and what are they doing?"
…

Read the whole file at its exact version.

How to install

The exact contents, by fingerprint

mdr add ammawla/encode-toolkit/regulatory-elements@sha256:5d1993bfd3bfdb64

The line at the top of this page pins the label git:20260920.6050003, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.

Badge

[![mdr](https://markdownregistry.com/badge/art_lhzcdqct5m6vofpf.svg)](https://markdownregistry.com/a/art_lhzcdqct5m6vofpf)

2 badge image fetches in 30 days. What the badge shows.

Versions

The registry has recorded 3 versions of this file, between Mar 8, 2026 and Sep 20, 2026, about one every 98 days.

version	committed	commit	size	audit
git:20260920.6050003 latest	2026-09-20	6050003	27,702 B	A	view · diff
git:20260920.992a807	2026-09-20	992a807	27,114 B	A	view · diff
git:20260308.ca46af5	2026-03-08	ca46af5	27,126 B	A	view

Audit of the latest version

A 17 of 17 checks passed. Fixed automatic checks with no AI involved, so the same checks give the same answer every run.

pass: Frontmatter block present
pass: Frontmatter declares a name
pass: Frontmatter declares a description
pass: Size between 200 bytes and 200 KB (27702 bytes)
pass: No zero-width or bidi control characters
pass: No instruction hidden inside an HTML comment
pass: No link to an exfiltration or paste host
pass: No credential-shaped string
pass: No instruction to send local credentials anywhere
pass: No text hidden with inline styles
pass: No prompt-injection phrasing
pass: No curl or wget piped into a shell
pass: No recursive delete of root, home or parent
pass: No instruction to read or print local credentials
pass: No base64 blob over 200 characters
pass: No link to a raw IP address
pass: No script tag

Source

GitHub

ammawla/encode-toolkit · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main

API

GET https://markdownregistry.com/api/v1/artifacts/art_lhzcdqct5m6vofpf
GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/regulatory-elements
GET https://markdownregistry.com/api/v1/blob/5d1993bfd3bfdb64640a8fd07717c28199e22c9b2f2e2a4e4fc7ac067aa3275c

Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.

Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.

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