ucsc-browser skillA
ucsc-browser is agent-read markdown (skill) from ammawla/encode-toolkit: 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..
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
# 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
mdr add ammawla/encode-toolkit/ucsc-browser@git:20260920.6050003mdr add ammawla/encode-toolkit/ucsc-browser@sha256:8096b5cc4cd754eePin 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_ajyucus2cdkrakzq)
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Versions
| 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
- 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
ammawla/encode-toolkit · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · 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
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