bio-atac-seq-consensus-peakset SKILL.md skillA
bio-atac-seq-consensus-peakset 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-atac-seq-consensus-peakset@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-atac-seq-consensus-peakset/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 20,268 bytes
- Repository stars
- 662
- License
- MIT
Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and majority-rule overlap. Use when generating a stable peak coordinate system for downstream differential accessibility, ML feature engineering, cross-sample comparison, or fixed-width peak counts; covers Corces 2018 iterative overlap (501 bp), DiffBind summit re-centering, and ENCODE consistency rules.
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: bedtools 2.31+, samtools 1.19+, BEDOPS 2.4.41+, GenomicRanges 1.54+, DiffBind 3.12+, Subread 2.0.2+ (featureCounts; `--countReadPairs` requires >= 2.0.2), pybedtools 0.10+.
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 unexpected errors, introspect the installed package and adapt rather than retrying.
# Consensus Peakset Construction
**"Build a single peakset to count reads against for all my samples"** -> Combine per-replicate or per-condition peak calls into a non-redundant, fixed-width set of regions. The strategy chosen drives FDR calibration, peak-width fairness, and reproducibility downstream.
- CLI: `bedtools merge` (simple union) and `bedtools multiinter` (per-sample membership columns emitted by default)
- CLI: Corces 2018 iterative overlap removal (custom shell)
- R: `DiffBind::dba.count(summits=250)` (built-in fixed-width)
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-atac-seq-consensus-peakset@sha256:8d529fbc133e3890The 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_5fk5kmzkh6cc4ffg)
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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 instruction to send local credentials anywhere
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- pass: No instruction to read or print local credentials
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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_5fk5kmzkh6cc4ffg GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-atac-seq-consensus-peakset GET https://markdownregistry.com/api/v1/blob/8d529fbc133e38905a9c8e9d3f91d6a8432f4fcd5cd398b6d682f5405165134e
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.