Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add GPTomics/bioSkills --skill oncoprint-mutation-matricesgit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/gptomics/bioskills/oncoprint-mutation-matrices)<a href="https://agentmods.dev/skills/gptomics/bioskills/oncoprint-mutation-matrices"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/oncoprint-mutation-matrices/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/gptomics/bioskills/oncoprint-mutation-matrices"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/oncoprint-mutation-matrices.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00095 | $0.03654 |
| Opus 5 | $0.00048 | $0.01827 |
| Sonnet 5 | $0.00019 | $0.00731 |
| Haiku 4.5 | $0.00010 | $0.00365 |
Grade A, and why
bio-data-visualization-oncoprint-mutation-matrices scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 8d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
Copies of this mod
1 near-identical copy found in the catalogue:
- bio-data-visualization-oncoprint-mutation-matrices — 97% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 277 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: ComplexHeatmap 2.18+, maftools 2.18+, comut 0.0.3+, MAFtools requires R 4.0+; comut.py requires pandas 2.0+, matplotlib 3.8+.
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - R:
packageVersion('<pkg>')then?function_name
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
OncoPrint and Mutation Matrix Plots
"Plot mutations across a cohort" -> Render a gene-by-sample matrix where each cell stacks colored rectangles encoding alteration class (missense, truncating, splice, copy-gain, copy-loss, fusion). Sort samples by burden, optionally split by clinical group, and overlay co-mutation / mutual-exclusivity annotations. OncoPrint (Cerami 2012 Cancer Discov 2:401; canonical at cBioPortal) is the genre-defining visualization.
- R:
ComplexHeatmap::oncoPrint,maftools::oncoplot - Python:
comut.CoMut,cbioportal-style implementations
The Single Most Important Modern Insight -- Cell Stacking Encodes Multiple Alterations Per Cell
OncoPrint differs from a generic heatmap because each cell can encode multiple alterations simultaneously through stacked rectangles. A patient with both a missense and a copy-gain in TP53 shows one cell with two overlapping colored rectangles (e.g., green diamond inside red square). This stacking is the whole point — it preserves the multi-modal alteration landscape that flattening to a single category destroys.
In ComplexHeatmap's oncoPrint, the alter_fun argument is the rendering specification: a named list of functions, one per alteration class, each drawing its rectangle inside the cell. Get this right and the figure works; get it wrong and overlapping alterations are invisible.
Decision Tree by Cohort and Question
| Question | Sort by | Display |
|---|---|---|
| Which genes are most altered? | Gene frequency (default) | Bar above samples (sample TMB); bar right of genes (gene frequency) |
| Per-patient burden patterns | Sample burden | TMB bar on top; sample-name labels |
| Subtype-driver enrichment | Clinical group then burden | column_split by group; per-group frequency right bar |
| Mutual exclusivity (BRAF vs NRAS) | Custom (alphabetic-by-mutation pattern) | Memo sort; overlay log10(OR) heatmap |
| Co-occurrence (TP53 + MYC) | Custom | Same pattern; positive OR coloring |
| Driver vs passenger comparison | Two panels | Concatenate two oncoPrints horizontally |
What ships with it
2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 8d ago First seen · 277 lines · 95 tokens per session scan A fd10f1730e20
bio-data-visualization-oncoprint-mutation-matrices is a skill published in the GitHub repository GPTomics/bioSkills (1,201 stars, last pushed 27d ago), licensed MIT. It adds 95 tokens to every session and 3,654 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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