bio-clip-seq-crosslink-site-detection SKILL.md skillA
bio-clip-seq-crosslink-site-detection 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-crosslink-site-detection@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-crosslink-site-detection/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 20,156 bytes
- Repository stars
- 662
- License
- MIT
Detect single-nucleotide crosslink (CL) sites in CLIP-seq data using truncation patterns (iCLIP/eCLIP CITS), crosslink-induced mutations (HITS-CLIP CIMS deletions, PAR-CLIP T-to-C), or HMM/kernel-density methods (PureCLIP, PARalyzer, CTK). Use when single-nucleotide resolution is required for motif registration (mCross), allele-specific binding (BEAPR), variant-effect prediction, or comparing crosslink chemistry across CLIP variants.
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: PureCLIP 1.3.1+, CTK 1.1.4+, PARalyzer 1.5+, wavClusteR 2.34+, pyCRAC 1.5+, samtools 1.19+, bedtools 2.31+, pysam 0.22+, R 4.3+.
Before using code patterns, verify installed versions match. If versions differ:
- CLI: `<tool> --version` then `<tool> --help` to confirm flags
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If code throws unexpected errors, introspect the installed tool and adapt the example to match the actual CLI rather than retrying.
# CLIP-seq Crosslink-Site Detection
**"Detect single-nucleotide crosslink sites in my CLIP data"** -> Identify the exact base where the protein-RNA UV adduct caused the reverse transcriptase to stop (truncation, in iCLIP/eCLIP), to read through with a mutation (deletion in HITS-CLIP, T->C in PAR-CLIP), or to leave a multi-base signature (PARalyzer kernel density for PAR-CLIP). Single-nucleotide resolution is the foundation of motif registration (mCross), allele-specific binding (BEAPR/ASPRIN), variant-effect prediction, and the most rigorous comparisons across CLIP…
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-clip-seq-crosslink-site-detection@sha256:8f10ef702d688f8cThe 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_acruscj4qjqnrelb)
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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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- pass: No zero-width or bidi control characters
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- pass: No link to an exfiltration or paste host
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- pass: No instruction to send local credentials anywhere
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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_acruscj4qjqnrelb GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-clip-seq-crosslink-site-detection GET https://markdownregistry.com/api/v1/blob/8f10ef702d688f8c45ec6cc839888ab0856072ec0d0a45923557f41559805732
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.