motif-analysis skillA
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motif-analysis is agent-read markdown (skill) from ammawla/encode-toolkit: 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..
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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 | |-----------|---------|-----------------|-----|-----------| …
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How to install
mdr add ammawla/encode-toolkit/motif-analysis@git:20260920.6050003mdr add ammawla/encode-toolkit/motif-analysis@sha256:097bd1b135789b80Pin 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_dz5jivuonuwusdzg)
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Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 21,635 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 21,144 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 21,139 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 · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_dz5jivuonuwusdzg GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/motif-analysis GET https://markdownregistry.com/api/v1/blob/097bd1b135789b80a7ce5524280b9742fa490ec625aa083ce0815a454ae092e2
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