bio-atac-seq-nucleosome-positioning SKILL.md skillA
bio-atac-seq-nucleosome-positioning 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-atac-seq-nucleosome-positioning@git:20260517.81511a7Pins git:20260517.81511a7 in mdr.lock. Pin the fingerprint instead.
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skills/bio-atac-seq-nucleosome-positioning/SKILL.md- Versions recorded
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- git:20260517.81511a7, committed May 17, 2026
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- a license file GitHub does not identify
Extract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and fragment analysis. Use when analyzing chromatin organization, identifying nucleosome-free regions at promoters, or characterizing nucleosome occupancy patterns from ATAC-seq fragment size distributions.
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: Rsamtools 2.18+, matplotlib 3.8+, numpy 1.26+, pyBigWig 0.3+, 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.
# Nucleosome Positioning
**"Map nucleosome positions from ATAC-seq"** → Separate nucleosome-free and mono-nucleosome fragments by size, then call nucleosome center positions and occupancy scores.
- CLI: `nucleoatac run --bed peaks.bed --bam atac.bam --fasta ref.fa`
- R: `ATACseqQC::splitGAlignmentsByCut()` for fragment separation
Extract nucleosome positions and occupancy from ATAC-seq fragment size patterns.
## Background
ATAC-seq fragments reflect chromatin structure:
- **< 100 bp**: Nucleosome-free regions (NFR)
- **180-247 bp**: Mono-nucleosome
- **315-473 bp**: Di-nucleosome
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How to install
mdr add fridrichmethod/awesome-skills/bio-atac-seq-nucleosome-positioning@sha256:24f5b9dc8025dcb0The 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_bo6p3zhgsox5eb66)
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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
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