peak-annotation SKILL.md skillA
peak-annotation from ammawla/encode-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add ammawla/encode-toolkit/peak-annotation@git:20260920.6050003Pins 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/peak-annotation/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260920.6050003, committed Sep 20, 2026
- First version recorded
- Mar 8, 2026
- Size
- 21,126 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Guide for annotating ENCODE peaks with genomic features using ChIPseeker and GREAT. Use when users need to assign peaks to genes, determine genomic feature distribution (promoter, intron, intergenic), or perform gene ontology enrichment of peak-associated genes. Trigger on: peak annotation, ChIPseeker, GREAT, peak to gene, genomic feature, promoter enrichment, gene ontology, peak distribution, TSS distance, nearest gene.
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
# Peak Annotation of ENCODE Data ## When to Use - User wants to annotate genomic peaks with nearby genes, regulatory features, or functional categories - User asks about "peak annotation", "ChIPseeker", "gene assignment", or "peak-to-gene mapping" - User needs to classify peaks as promoter, enhancer, intronic, intergenic, etc. - User wants to run GO/pathway enrichment on genes near their peaks - Example queries: "annotate my H3K27ac peaks with nearby genes", "what genes are near these ATAC-seq peaks?", "run pathway analysis on peak-associated genes" Help the user annotate ENCODE peak calls with genomic features and functional enrichment. Peak annotation bridges the gap between regulatory elements (peaks) and biological function (genes, pathways). This skill covers two complementary approaches: ChIPseeker for genomic feature annotation and visualization, and GREAT for functional enrichment analysis of non-coding regions. ## Literature Foundation | Reference | Journal | Key Contribution | DOI | Citations | |-----------|---------|-----------------|-----|-----------| …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/peak-annotation@sha256:9c26b29e3ef8de63The 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.
[](https://markdownregistry.com/a/art_7mqoztgltay3rsmb)
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Versions
The registry has recorded 5 versions of this file, between Mar 8, 2026 and Sep 20, 2026, about one every 49 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 21,126 B | A | view · diff |
| git:20260920.992a807 | 2026-09-20 | 992a807 | 20,958 B | A | view · diff |
| git:20260920.f517fca | 2026-09-20 | f517fca | 20,953 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 20,971 B | A | view · diff |
| git:20260308.ca46af5 | 2026-03-08 | ca46af5 | 20,982 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 (21126 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 · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_7mqoztgltay3rsmb GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/peak-annotation GET https://markdownregistry.com/api/v1/blob/9c26b29e3ef8de635214c6ea84a5989c529f10e12a74e1206523b0a76d914072
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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