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 LigphiDonk/Oh-my--paper --skill bioinformatics-init-analysisgit clone --depth 1 https://github.com/LigphiDonk/Oh-my--paperWrote 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/ligphidonk/oh-my--paper/bioinformatics-init-analysis)<a href="https://agentmods.dev/skills/ligphidonk/oh-my--paper/bioinformatics-init-analysis"><img src="https://agentmods.dev/badge/skills/ligphidonk/oh-my--paper/bioinformatics-init-analysis/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/ligphidonk/oh-my--paper/bioinformatics-init-analysis"><img src="https://agentmods.dev/badge/skills/ligphidonk/oh-my--paper/bioinformatics-init-analysis.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 1 finding, up to medium
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- medium Rogue Agent · line 54 Skill establishes unauthorized persistence across sessions via cron jobs, startup scripts, or state files. Session persistence allows an attacker to maintain access beyond the current interaction.Fix: Remove any persistence mechanisms (cron jobs, startup scripts, state files). Skills should not maintain state across sessions without explicit user consent.
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 | $0.00010 | $0.01302 |
| Opus 5 | $0.00005 | $0.00651 |
| Sonnet 5 | $0.00002 | $0.00260 |
| Haiku 4.5 | $0.00001 | $0.00130 |
Grade A, and why
bioinformatics-init-analysis 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 10d 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.
How it starts
The opening of the file, as written. The whole thing — 160 lines — stays where its author put it; the contents beside it link to each section on GitHub.
bioinformatics-init-analysis
Canonical Summary
bioinformatics-init-analysis
Trigger Rules
Use this skill when the user request matches its research workflow scope. Prefer the bundled resources instead of recreating templates or reference material. Keep outputs traceable to project files, citations, scripts, or upstream evidence.
Resource Use Rules
- Read from
references/only when the current task needs the extra detail. - Treat
scripts/as optional helpers. Run them only when their dependencies are available, keep outputs in the project workspace, and explain a manual fallback if execution is blocked.
Execution Contract
- Resolve every relative path from this skill directory first.
- Prefer inspection before mutation when invoking bundled scripts.
- If a required runtime, CLI, credential, or API is unavailable, explain the blocker and continue with the best manual fallback instead of silently skipping the step.
- Do not write generated artifacts back into the skill directory; save them inside the active project workspace.
Upstream Instructions
bioinformatics-init-analysis
A Claude Code plugin that automates initial data analysis for high-dimensional single-cell biology data. Supports CyTOF (mass cytometry), scRNA-seq, and flow cytometry with automatic data type detection and plain-language clinical report generation.
Features
- 7-step pipeline: Load → QC → Normalize → PCA/UMAP → Cluster → Marker Analysis → Report
- Auto-detection: Identifies CyTOF, scRNA-seq, or flow cytometry from file format and marker patterns
- Clinical reports: HTML reports with plain-language explanations for medical doctors and non-bioinformaticians
- Data-type-aware: QC, normalization, and interpretation adapt to data type
- Modular: Run the full pipeline or import individual steps
Installation
Clone into your Claude Code plugins directory:
git clone https://github.com/<your-username>/bioinformatics-init-analysis.git \
~/.claude/plugins/bioinformatics-init-analysis
What ships with it
16 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.
- README.md 3.6 KB
- references/cytof_specifics.md 3.3 KB
- references/plot_interpretation_guide.md 7.7 KB
- references/scrnaseq_specifics.md 3.8 KB
- references/statistical_methods.md 8.2 KB
- scripts/detect_data_type.py 3.4 KB runs code
- scripts/run_pipeline.py 5.1 KB runs code
- scripts/step1_load_data.py 6.7 KB runs code
- scripts/step2_qc.py 6.6 KB runs code
- scripts/step3_normalize.py 4.7 KB runs code
- scripts/step4_dim_reduction.py 6.1 KB runs code
- scripts/step5_clustering.py 4.9 KB runs code
- scripts/step6_marker_analysis.py 9.0 KB runs code
- scripts/step7_report.py 21 KB runs code
- scripts/utils.py 4.6 KB runs code
- skills/init-analysis/SKILL.md 5.4 KB
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.
- 10d ago First seen · 160 lines · 10 tokens per session scan A 3c543d11abe1
bioinformatics-init-analysis is a skill published in the GitHub repository LigphiDonk/Oh-my--paper (721 stars, last pushed 4mo ago), licensed MIT. It adds 10 tokens to every session and 1,302 once invoked, about $0.0001 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 2026-08-30.
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