bio-clip-seq-clip-motif-analysis SKILL.md skillA
bio-clip-seq-clip-motif-analysis from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-clip-seq-clip-motif-analysis@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-clip-seq-clip-motif-analysis/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 22,230 bytes
- Repository stars
- 662
- License
- MIT
Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo, mCross (CL-position-registered motifs), PEKA (positional k-mer enrichment), RBPamp (affinity), and RNA Bind-n-Seq (RBNS) cross-validation. Use when characterizing RBP sequence specificity, registering motifs to crosslink positions, validating in vivo CLIP motifs against in vitro RBNS Kd, reconciling motif disagreements across tools, or correcting for the uracil crosslinking…
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
## Version Compatibility Reference examples tested with: HOMER 4.11+, MEME Suite 5.5+ (STREME, MEME-ChIP, FIMO), bedtools 2.31+, kpLogo 1.1+, mCross v1+, PEKA v1+, RBPamp 0.9+, ggseqlogo 0.1+, biopython 1.83+. Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws unexpected errors, introspect the installed tool and adapt the example to match the actual API rather than retrying. # CLIP-seq Motif Analysis **"Find enriched RNA motifs at my RBP binding sites"** -> Discover the in vivo sequence preference of an RNA-binding protein from CLIP-seq peaks or single-nucleotide crosslink sites. The fundamental confound is the uracil bias of UV254 crosslinking: U is the most-crosslinked base, so naive motif logos centered on CL positions are U-enriched even for non-U-binding RBPs. Modern tools (mCross, PEKA) register motifs relative to the CL position and correct for this bias; legacy tools (HOMER, MEME) need careful background selection. …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-clip-seq-clip-motif-analysis@sha256:fb78a3ecae49063aThe line at the top of this page pins the label git:20260821.2d1b678, 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_v45mc4r6phkpo2jc)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_v45mc4r6phkpo2jc GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-clip-seq-clip-motif-analysis GET https://markdownregistry.com/api/v1/blob/fb78a3ecae49063a2015cc00275b36c662aec8d9d477b268501c5a089efcb941
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.