bio-chipseq-qc SKILL.md skillA
bio-chipseq-qc 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-chipseq-qc@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-chip-seq-chipseq-qc/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 17,755 bytes
- Repository stars
- 662
- License
- MIT
Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE…
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: deepTools 3.5+, phantompeakqualtools 1.2.2+, ChIPQC 1.42+, IDR 2.0.4+, samtools 1.19+, bedtools 2.31+, pysam 0.22+, pybedtools 0.9+, MACS2 2.2.9+, MACS3 3.0.4+. Verify versions before relying on numerical thresholds — phantompeakqualtools has known R-version compatibility issues with R ≥ 4.0 (use kundajelab fork or pin to R 3.6). # ChIP-seq Quality Control **"Should I trust this ChIP-seq experiment?"** -> Validate antibody, fragmentation, enrichment, replicate concordance, library complexity, and absence of hyper-ChIPable artifacts before committing to downstream peak calling and differential analysis. - CLI: `Rscript run_spp.R -c=chip.bam -out=cc.txt` (NSC/RSC), `plotFingerprint -b chip.bam input.bam` (enrichment shape), `idr --samples rep1.np rep2.np` (replicate IDR) - R: ChIPQC package (Carroll & Stark; computes the full ENCODE metric battery) - Python: pysam + pybedtools for custom FRiP and library-complexity metrics ChIP-seq fails for many independent reasons. The QC metrics below probe distinct failure modes — passing one metric does not rescue another. Antibody failure cannot be fixed by sequencing more. …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-chipseq-qc@sha256:a399fd3639e8e689The 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_gbpdbv6aj3c43lht)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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 (17755 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
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_gbpdbv6aj3c43lht GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-chipseq-qc GET https://markdownregistry.com/api/v1/blob/a399fd3639e8e689e701e71260451b1e3335f00a36d9f8d4743cf8a51e18b4aa
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.
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