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.