Borrowing it
Nothing to install: this file belongs to omar-A-hassan/medsci-agent. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/omar-A-hassan/medsci-agent/main/.opencode/skills/scanpy/SKILL.mdgit clone --depth 1 https://github.com/omar-A-hassan/medsci-agentWrote 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/omar-a-hassan/medsci-agent/scanpy)<a href="https://agentmods.dev/skills/omar-a-hassan/medsci-agent/scanpy"><img src="https://agentmods.dev/badge/skills/omar-a-hassan/medsci-agent/scanpy/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/omar-a-hassan/medsci-agent/scanpy"><img src="https://agentmods.dev/badge/skills/omar-a-hassan/medsci-agent/scanpy.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 | $0.00029 | $0.00383 |
| Opus 5 | $0.00015 | $0.00192 |
| Sonnet 5 | $0.00006 | $0.00077 |
| Haiku 4.5 | $0.00003 | $0.00038 |
Grade A, and why
scanpy 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 9d 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.
What it actually says
Scanpy — Single-Cell Analysis
When to Use
- Loading and exploring .h5ad (AnnData) files
- QC, filtering, normalization of single-cell data
- Cell clustering (Leiden/Louvain)
- Differential expression between clusters or conditions
- UMAP/t-SNE dimensionality reduction
Standard Pipeline
1. Read data → read_h5ad(path)
2. QC filtering → preprocess_omics(path, min_genes=200, min_cells=3)
3. Normalize → (included in preprocess step)
4. HVG select → (included in preprocess step, n_top_genes=2000)
5. Cluster → cluster_cells(path, method="leiden", resolution=1.0)
6. DE analysis → differential_expression(path, groupby="leiden")
7. Enrichment → gene_set_enrichment(genes=[...top DE genes])
Key Parameters
- resolution: Controls granularity of clustering. 0.4-0.8 for broad clusters, 1.0-2.0 for fine-grained
- min_genes: Cells with fewer genes are likely empty droplets (default 200)
- min_cells: Genes in fewer cells are likely noise (default 3)
- n_top_genes: Highly variable genes for downstream analysis (default 2000)
Interpreting Results
- Cluster sizes should be relatively balanced — very small clusters may be doublets
- DE genes with |log2FC| > 1 and padj < 0.05 are considered significant
- Check for batch effects before biological interpretation
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.
- 9d ago First seen · 37 lines · 29 tokens per session scan A 6211f34441a7
scanpy is a skill published in the GitHub repository omar-A-hassan/medsci-agent (18 stars, last pushed 2d ago), licensed MIT. It adds 29 tokens to every session and 383 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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