bio-atac-seq-nucleosome-positioning SKILL.md skillA
bio-atac-seq-nucleosome-positioning 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-nucleosome-positioning@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
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- SKILL.md skill
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- pku-yuangroup/openai4s
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skills/bioskills/bio-atac-seq-nucleosome-positioning/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
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- License
- MIT
Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter. Use when characterizing nucleosome organization at promoters and enhancers, calling +1/-1 nucleosomes flanking NFRs, generating V-plots for chromatin structure visualization, or comparing nucleosome positioning between conditions.
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: NucleoATAC 0.3.4+, ATACseqQC 1.26+, DANPOS 3.1+, samtools 1.19+, pysam 0.22+, pyBigWig 0.3+, BSgenome.Hsapiens.UCSC.hg38 1.4+, TxDb.Hsapiens.UCSC.hg38.knownGene 3.18+.
NucleoATAC is unmaintained since 2018 but remains the canonical ATAC-specific nucleosome caller; ATACseqQC, DANPOS3, and scprinter are actively developed alternatives. Verify versions before use:
- 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.
# Nucleosome Positioning
**"Where are the nucleosomes in my ATAC-seq data?"** -> Use fragment-size classes (Tn5 cuts twice through naked DNA generating short fragments; once on each side of a single nucleosome generating ~147+linker fragments) to call nucleosome centers, occupancy scores, and the spacing pattern around regulatory elements.
- CLI: `nucleoatac run --bed regions.bed --bam sample.bam --fasta genome.fa`
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How to install
mdr add pku-yuangroup/openai4s/bio-atac-seq-nucleosome-positioning@sha256:089c59468c8bff9aThe 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_3wizhh7dky2gbomz)
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The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
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