bio-copy-number-copy-ratio-segmentation SKILL.md skillA
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- SKILL.md skill
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- pku-yuangroup/openai4s
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skills/bioskills/bio-copy-number-copy-ratio-segmentation/SKILL.md- Versions recorded
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- git:20260821.2d1b678, committed Aug 21, 2026
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- MIT
Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (CBS, DNAcopy), hidden Markov models, HaarSeg, and fused-lasso methods. Covers GC-content, mappability, and replication-timing (wave-artifact) bias correction, panel-of-normals/PCA denoising, diploid-baseline centering, and algorithm selection by sequencing depth and event size. Use when choosing a segmentation algorithm, correcting depth bias, diagnosing oversegmentation or a…
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What the file says
## Version Compatibility
Reference examples tested with: R 4.3+ with DNAcopy 1.76+, Python 3.10+ with numpy 1.26+, pandas 2.2+; QDNAseq 1.38+ (optional, GC/mappability normalization).
Before using code patterns, verify installed versions match. If versions differ:
- R: `packageVersion('DNAcopy')` then `?segment` to confirm arguments
- Python: `pip show numpy pandas`
If code throws an error, introspect the installed package and adapt the example. CBS lives in Bioconductor `DNAcopy`; HMM segmentation is provided by caller-specific backends (CNVkit uses `pomegranate`; HaarSeg has its own R/Python packages).
# Copy-Ratio Segmentation
**"Turn noisy per-bin depth into clean copy-number segments"** -> Two stages, both error-prone. First, normalize the depth profile so the only remaining variation is copy number (not GC, mappability, or replication timing). Second, partition the normalized profile into segments of constant copy number. The segmentation algorithm choice has a *predictable* bias signature, and the diploid-baseline choice can invert every call.
- R: `DNAcopy::segment` (CBS, the reference implementation)
- Python: HMM via `pomegranate`; HaarSeg via `haarseg`
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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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