bio-atac-seq-nucleosome-positioning skillA
bio-atac-seq-nucleosome-positioning is agent-read markdown (skill) from pku-yuangroup/openai4s: 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..
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: 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@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-atac-seq-nucleosome-positioning@sha256:089c59468c8bff9aPin 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_3wizhh7dky2gbomz)
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
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