bio-chipseq-qc SKILL.md skillA
bio-chipseq-qc from fridrichmethod/awesome-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fridrichmethod/awesome-skills/bio-chipseq-qc@git:20260517.81511a7Pins git:20260517.81511a7 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fridrichmethod/awesome-skills
- Path
skills/bio-chipseq-qc/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260517.81511a7, committed May 17, 2026
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- 15
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- a license file GitHub does not identify
ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate concordance. Use to assess experiment quality before downstream analysis. Use when assessing ChIP-seq data quality metrics.
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: MACS3 3.0+, Subread 2.0+, bedtools 2.31+, deepTools 3.5+, pybedtools 0.9+, pysam 0.22+, samtools 1.19+
Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show <package>` then `help(module.function)` to check signatures
- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
- CLI: `<tool> --version` then `<tool> --help` to confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed
package and adapt the example to match the actual API rather than retrying.
# ChIP-seq Quality Control
**"Assess the quality of my ChIP-seq experiment"** → Compute FRiP, cross-correlation (NSC/RSC), library complexity, and IDR replicate concordance to evaluate enrichment success.
- CLI: `deeptools plotFingerprint`, `phantompeakqualtools run_spp.R`
- Python: `pysam` + `pybedtools` for custom QC metrics
Quality metrics for assessing ChIP-seq experiment success and replicate reproducibility.
## FRiP (Fraction of Reads in Peaks)
**Goal:** Quantify enrichment strength by measuring the proportion of reads falling within called peaks.
…Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-chipseq-qc@sha256:27a8787a913413f5The line at the top of this page pins the label git:20260517.81511a7, 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_n7cb5dpgq7qi5szt)
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Versions
The registry has recorded 1 version of this file, committed on May 17, 2026.
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Source
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_n7cb5dpgq7qi5szt GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-chipseq-qc GET https://markdownregistry.com/api/v1/blob/27a8787a913413f53211cc847bbb4b182e318febed932546f37f38d5625f5983
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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