motif-analysis SKILL.md skillA
motif-analysis 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/motif-analysis@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/motif-analysis/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260920.6050003, committed Sep 20, 2026
- First version recorded
- Mar 8, 2026
- Size
- 21,635 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Guide for de novo and known motif enrichment analysis of ENCODE ChIP-seq and ATAC-seq peaks using HOMER and MEME Suite. Use when users need to discover TF binding motifs in peaks, validate ChIP-seq targets, or find co-binding partners. Trigger on: motif analysis, HOMER, MEME, de novo motif, motif enrichment, findMotifsGenome, AME, MEME-ChIP, known motif, TF binding motif, co-factor, motif discovery.
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
# Motif Analysis of ENCODE Peak Data ## When to Use - User wants to discover transcription factor binding motifs in ChIP-seq or ATAC-seq peaks - User asks about "motif enrichment", "HOMER", "MEME", or "de novo motif discovery" - User needs to validate ChIP-seq targets by checking if the expected motif is enriched - User wants to find co-binding partners or co-factor motifs in peak regions - Example queries: "find motifs in my CTCF peaks", "run HOMER on ATAC-seq peaks", "what TFs co-bind with p300 in liver?" Help the user perform de novo and known motif enrichment analysis on ENCODE ChIP-seq and ATAC-seq peaks. Motif analysis serves two critical purposes: (1) validating that ChIP-seq experiments pulled down the expected transcription factor, and (2) discovering co-regulatory partners that co-bind with the target factor. This skill covers the two major tool suites -- HOMER and MEME Suite -- from input preparation through result interpretation. ## Literature Foundation | Reference | Journal | Key Contribution | DOI | Citations | |-----------|---------|-----------------|-----|-----------| …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/motif-analysis@sha256:097bd1b135789b80The 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_d3a7e6dpn6oy42mn)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between Mar 8, 2026 and Sep 20, 2026, about one every 65 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 21,635 B | A | view · diff |
| git:20260920.992a807 | 2026-09-20 | 992a807 | 21,144 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 21,139 B | A | view · diff |
| git:20260308.ca46af5 | 2026-03-08 | ca46af5 | 21,150 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 (21635 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_d3a7e6dpn6oy42mn GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/motif-analysis GET https://markdownregistry.com/api/v1/blob/097bd1b135789b80a7ce5524280b9742fa490ec625aa083ce0815a454ae092e2
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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