homer-motif-analysis SKILL.md skillA
homer-motif-analysis from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/homer-motif-analysis@git:20260929.7a7d60fPins git:20260929.7a7d60f in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/homer-motif-analysis/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- Feb 18, 2026
- Size
- 25,744 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
De novo and known TF motif enrichment in ChIP-seq/ATAC-seq peaks via HOMER. findMotifsGenome.pl finds over-represented patterns vs background; annotatePeaks.pl assigns context (TSS distance, gene, repeat). Use after MACS3 to identify enriched TFs, annotate peaks with nearest genes, and validate ChIP-seq via the target motif.
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
# HOMER — Motif Analysis and Peak Annotation ## Overview HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of Perl/C++ tools for analyzing genomic regulatory elements. Its two primary commands are `findMotifsGenome.pl`, which performs de novo motif discovery and known motif enrichment against JASPAR/HOMER databases, and `annotatePeaks.pl`, which maps each peak to the nearest gene, distance to TSS, and genomic feature class (promoter, intron, intergenic, repeat). HOMER takes BED-format peak files from MACS3 or similar peak callers and a reference genome assembly as input, and outputs HTML/text reports ranking enriched motifs by p-value and fold enrichment over a matched background. ## When to Use - Identifying which transcription factors are bound in a ChIP-seq peak set by enriching their known motifs from JASPAR or the HOMER motif library - Discovering novel sequence motifs de novo in open chromatin regions from ATAC-seq without prior knowledge of the binding TF - Comparing motif landscapes between two conditions (e.g., treated vs. untreated peak sets) by running HOMER with one set as target and the other as background …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/homer-motif-analysis@sha256:0e8b7f8bc1621372The line at the top of this page pins the label git:20260929.7a7d60f, 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_xnv6c4r7hbuickv3)
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Versions
The registry has recorded 5 versions of this file, between Feb 18, 2026 and Sep 29, 2026, about one every 56 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.7a7d60f latest | 2026-09-29 | 7a7d60f | 25,744 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 25,793 B | A | view · diff |
| git:20260428.81ea2d2 | 2026-04-28 | 81ea2d2 | 23,458 B | A | view · diff |
| git:20260414.65bebbb | 2026-04-14 | 65bebbb | 23,595 B | A | view · diff |
| git:20260218.8df1694 | 2026-02-18 | 8df1694 | 23,235 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 (25744 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
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_xnv6c4r7hbuickv3 GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/homer-motif-analysis GET https://markdownregistry.com/api/v1/blob/0e8b7f8bc1621372ab1f30dd532af2097ad755401bd2779ae142f6b1ac524b91
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.