bio-clip-seq-differential-clip SKILL.md skillA
bio-clip-seq-differential-clip 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-differential-clip@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-differential-clip/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 23,600 bytes
- Repository stars
- 662
- License
- MIT
Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper (Skipper-downstream), ASpeak, edgeR, or limma-voom. Use when computing condition-level changes in RBP binding intensity, choosing peak-level vs window-level vs crosslink-level testing, designing replicate experiments, or distinguishing biological binding shifts from technical confounders.
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: DEWSeq 1.18+, htseq-clip 2.0+, DESeq2 1.44+, edgeR 4.2+, limma 3.60+, Flipper (commit 2024.04+), Skipper (commit 2023.05+), pybedtools 0.10+, pyranges 0.0.129+.
Before using code patterns, verify installed versions match. If versions differ:
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If code throws unexpected errors, introspect the installed package and adapt the example to match the actual API rather than retrying.
# Differential CLIP-seq Analysis
**"Identify regions with changed RBP binding across conditions"** -> Test for condition-level differences in IP enrichment relative to SMInput, accounting for replicate variance and (where available) sequencing depth normalization. Three statistical scales are possible: peak-level (test each peak as a unit), window-level (test fixed transcriptome windows; DEWSeq, Flipper), or crosslink-site level (test single-nt positions). The choice depends on the biology (narrow regulatory shift vs broad binding-mode…
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-clip-seq-differential-clip@sha256:3e42c3997e10d989The 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_n2nb5a4paelt2rkm)
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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 instruction hidden inside an HTML comment
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- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
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- 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
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- pass: No script tag
Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_n2nb5a4paelt2rkm GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-clip-seq-differential-clip GET https://markdownregistry.com/api/v1/blob/3e42c3997e10d989a3e228d61af9120583a692736789eb0d17600d3f4448be94
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.