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bio-copy-number-cnv-visualization

Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or deciding what depth-only plots cannot reveal.

BioTender-maxgithub.com/BioTender-maxGitHub ↗
claude-codeships scriptsNOASSERTION
Install
npx skills add BioTender-max/awesome-bio-agent-skills --skill cnv-visualization --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

Facts
Files in the skill folder: 3
SKILL.md size: 13 KB
Bundled scripts: yes
Path: skills/bioskills/cnv-visualization/SKILL.md
Open the folder on GitHub →
Where it comes from
Stars: 135
Language: Python

Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.

From the SKILL.md

## Version Compatibility Reference examples tested with: matplotlib 3.8+, pandas 2.2+, numpy 1.26+, seaborn 0.13+, CNVkit 0.9.10+, GATK 4.5+; R 4.3+ with ggplot2 3.5+. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show matplotlib pandas` then `help(function)` for signatures - R: `packageVersion('ggplot2')` then `?function_name` - CLI: `cnvkit.py version`, `gatk --version` If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example rather than retrying. # CNV Visualization **"Plot my copy number profile"** -> A CNV figure is an argument, not a picture. The plot type, the y-axis quantity, and where the diploid baseline sits all determine what the reader can conclude. The single most important rule: a depth-only log2 plot cannot show loss of heterozygosity, cannot show tumor purity, and silently misleads if the diploid baseline is centered on a non-diploid mode. - CLI: `cnvkit.py scatter` / `diagram` / `heatmap`; `gatk PlotModeledSegments` - Python: `matplotlib` for custom genome-wide and allele-specific tracks - R: `ggplot2`, `karyoploteR` for publication ideograms ## Plot Selection

What's inside
Steps it walks through
  1. Version Compatibility
  2. Plot Selection — What Each View Reveals and Hides
  3. CNVkit Built-in Plots
  4. Genome-Wide log2 Profile with Segments
  5. Combined log2 + B-Allele-Frequency Panel
  6. Cohort Heatmap
  7. Caller-Native Diagnostic Plots
  8. Failure Modes
  9. The diploid-baseline centering trap
  10. log2 axis presented as if it were absolute copy number
  11. Cohort heatmap binning erases focal events
  12. Quantitative Thresholds
  13. Common Errors
  14. References
Ships with 2 files
  • examples/plot_cnv.py
  • usage-guide.md
Commands it runs
cnvkit.py scatter sample.cnr -s sample.cns -o scatter.png            # genome-wide
cnvkit.py scatter sample.cnr -s sample.cns -c chr17 -o chr17.png      # one chromosome
cnvkit.py scatter sample.cnr -s sample.cns -v sample.vcf.gz -o baf.png  # with BAF panel
cnvkit.py diagram sample.cnr -s sample.cns -o diagram.pdf             # ideogram
cnvkit.py heatmap cohort/*.cns -d -o cohort_heatmap.pdf              # cohort, desaturated
gatk PlotModeledSegments --denoised-copy-ratios tumor.denoisedCR.tsv \
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About this skill
What does the bio-copy-number-cnv-visualization skill do?

Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or deciding what depth-only plots cannot reveal.

How do I install it?

Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill cnv-visualization --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.

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