bio-atac-seq-nucleosome-positioning
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-nucleosome-positioning --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## 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 - **558-
- Version Compatibility
- Background
- ATACseqQC (R)
- Installation
- Fragment Size Distribution
- Nucleosome Positioning
- V-Plot (Fragment Size vs Position)
- Footprinting
- NucleoATAC (Python)
- Run NucleoATAC
- Output Files
- Visualize Output
- Fragment Analysis (Custom)
- Extract Fragment Sizes
pip install nucleoatac Call nucleosomes nucleoatac run --bed regions.bed --bam sample.bam --fasta reference.fa \ Convert to bigWig for visualization bedGraphToBigWig nucleoatac_output.occ.bedgraph chrom.sizes nucleosome_occ.bw Extract nucleosome-free reads samtools view -h sample.bam | \ awk '$9 > -100 && $9 < 100 || $1 ~ /^@/' | \ samtools view -b > nfr.bam Extract mono-nucleosome reads
What does the bio-atac-seq-nucleosome-positioning skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-nucleosome-positioning --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.