peak-annotation skillA
peak-annotation is agent-read markdown (skill) from ammawla/encode-toolkit: 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..
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
# 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@git:20260920.6050003mdr add ammawla/encode-toolkit/peak-annotation@sha256:9c26b29e3ef8de63Pin 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_uqg5rtnto72okhmf)
1 badge views in 30 days
Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 21,126 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 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 |
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 · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_uqg5rtnto72okhmf GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/peak-annotation GET https://markdownregistry.com/api/v1/blob/9c26b29e3ef8de635214c6ea84a5989c529f10e12a74e1206523b0a76d914072
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.