bio-atac-seq-consensus-peakset skillA
bio-atac-seq-consensus-peakset is agent-read markdown (skill) from pku-yuangroup/openai4s: 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..
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns 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@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-atac-seq-consensus-peakset@sha256:8d529fbc133e3890Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_5fk5kmzkh6cc4ffg)
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · 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
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