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ucsc-browser SKILL.md skillA

ucsc-browser 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/ucsc-browser@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: plugin/skills/ucsc-browser/SKILL.md
Versions recorded: 3
Latest version: git:20260920.6050003, committed Sep 20, 2026
First version recorded: Mar 12, 2026
Size: 17,018 bytes
Repository stars: 21
License: AGPL-3.0

Query the UCSC Genome Browser REST API to retrieve regulatory tracks, DNA sequences, cCRE annotations, TF binding clusters, and track schemas for any genomic region. Use when the user wants to look up what regulatory elements exist at a genomic locus, retrieve DNA sequence under peaks, query ENCODE cCREs or TF rPeak clusters from UCSC, check what tracks are available for a genome assembly, get chromatin accessibility across cell types, or cross-reference ENCODE data with UCSC-hosted annotations.

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

# Query the UCSC Genome Browser REST API

## When to Use

- User wants to query the UCSC Genome Browser REST API for tracks, sequences, or cCRE annotations
- User asks about "UCSC", "genome browser", "cCREs", "track hub", or "sequence retrieval"
- User needs to retrieve DNA sequences for peak regions or regulatory elements
- User wants to intersect ENCODE peaks with UCSC-hosted annotations (cCREs, conservation, repeat masker)
- Example queries: "get cCRE annotations for my region", "fetch DNA sequence under my peaks", "query UCSC for conservation scores at my enhancers"

Retrieve regulatory annotations, DNA sequences, TF binding data, and ENCODE-hosted tracks from the UCSC Genome Browser programmatic interface.

## Scientific Rationale

**The question**: "What regulatory annotations exist at this genomic locus, and what is the underlying sequence?"
…

Read the whole file at its exact version.

How to install

The exact contents, by fingerprint

mdr add ammawla/encode-toolkit/ucsc-browser@sha256:8096b5cc4cd754ee

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_ajyucus2cdkrakzq.svg)](https://markdownregistry.com/a/art_ajyucus2cdkrakzq)

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

Versions

The registry has recorded 3 versions of this file, between Mar 12, 2026 and Sep 20, 2026, about one every 96 days.

version	committed	commit	size	audit
git:20260920.6050003 latest	2026-09-20	6050003	17,018 B	A	view · diff
git:20260920.ce7840d	2026-09-20	ce7840d	16,597 B	A	view · diff
git:20260312.be32706	2026-03-12	be32706	16,586 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 (17018 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_ajyucus2cdkrakzq
GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/ucsc-browser
GET https://markdownregistry.com/api/v1/blob/8096b5cc4cd754eeb61ba4963f6eff84e9ad4bc62739d3a165a5259549da7a74

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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