regulatory-elements skillA
regulatory-elements is agent-read markdown (skill) from ammawla/encode-toolkit: 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 EN.
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns 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
mdr add ammawla/encode-toolkit/regulatory-elements@git:20260920.6050003mdr add ammawla/encode-toolkit/regulatory-elements@sha256:5d1993bfd3bfdb64Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_jrixkuxpvigfy3h7)
1 badge views in 30 days
Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 27,702 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 27,114 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 27,126 B | A | view |
Audit of the latest version
- 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
ammawla/encode-toolkit · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_jrixkuxpvigfy3h7 GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/regulatory-elements GET https://markdownregistry.com/api/v1/blob/5d1993bfd3bfdb64640a8fd07717c28199e22c9b2f2e2a4e4fc7ac067aa3275c
Your agent 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.