bio-copy-number-cnv-visualization
Visualize copy number profiles, segments, and compare across samples. Create publication-quality plots of CNV data from CNVkit, GATK, or other callers. Use when creating genome-wide CNV plots, sample heatmaps, or chromosome-level visualizations.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-copy-number-cnv-visualization --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: GATK 4.5+, ggplot2 3.5+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, seaborn 0.13+ 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. # CNV Visualization **"Plot my copy number profile"** → Create genome-wide scatter plots, segmentation views, and multi-sample heatmaps from CNV caller output. - CLI: `cnvkit.py scatter`, `cnvkit.py diagram`, `cnvkit.py heatmap` - Python: `matplotlib` for custom CNV plots - R: `ggplot2` for publication figures ## CNVkit Built-in Plots **Goal:** Generate standard CNV visualizations directly from CNVkit output files. **Approach:** Use CNVkit scatter, diagram, and heatmap commands for quick visual inspection. ```bash # Scatter plot with segments cnvkit.py scatter sample.cnr -s sample.cns -o scatter.
- Version Compatibility
- CNVkit Built-in Plots
- Python: Genome-wide Profile
- Python: Single Chromosome Plot
- Python: Cohort Heatmap
- R: ggplot2 Visualization
- Circos-style Plot
- GATK Plot Commands
- Related Skills
Scatter plot with segments cnvkit.py scatter sample.cnr -s sample.cns -o scatter.png Scatter for specific chromosome cnvkit.py scatter sample.cnr -s sample.cns -c chr17 -o chr17_scatter.png Ideogram diagram cnvkit.py diagram sample.cnr -s sample.cns -o diagram.pdf Heatmap across samples cnvkit.py heatmap *.cns -o cohort_heatmap.pdf Heatmap for specific region cnvkit.py heatmap *.cns -c chr17:7500000-7700000 -o tp53_region.pdf
What does the bio-copy-number-cnv-visualization skill do?
Visualize copy number profiles, segments, and compare across samples. Create publication-quality plots of CNV data from CNVkit, GATK, or other callers. Use when creating genome-wide CNV plots, sample heatmaps, or chromosome-level visualizations.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-copy-number-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 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.