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 agentlas-ai/agentlas-desktop --skill scanpygit clone --depth 1 https://github.com/agentlas-ai/agentlas-desktopWrote 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/agentlas-ai/agentlas-desktop/scanpy)<a href="https://agentmods.dev/skills/agentlas-ai/agentlas-desktop/scanpy"><img src="https://agentmods.dev/badge/skills/agentlas-ai/agentlas-desktop/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/agentlas-ai/agentlas-desktop/scanpy"><img src="https://agentmods.dev/badge/skills/agentlas-ai/agentlas-desktop/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 | $0.00093 | $0.04178 |
| Opus 5.5 | $0.00037 | $0.01671 |
| Sonnet 5.5 | $0.00019 | $0.00836 |
| Haiku 4.5 | $0.00009 | $0.00418 |
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 1mo 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.
This is a copy
100% identical to scanpy — 66 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 321 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Scanpy: Single-Cell Analysis
Overview
Scanpy is a scalable Python toolkit for analyzing single-cell RNA-seq data, built on AnnData. Apply this skill for complete single-cell workflows including quality control, normalization, dimensionality reduction, clustering, marker gene identification, visualization, and trajectory analysis. Current stable release: scanpy 1.12.x (January 2026).
Installation
Requires Python 3.12+ (scanpy 1.12 dropped Python ≤3.11) and anndata ≥0.10.
uv pip install "scanpy[leiden]"
The [leiden] extra installs python-igraph and leidenalg, required for Leiden clustering. For reproducible environments, pin a version: uv pip install "scanpy[leiden]==1.12.1".
For large or out-of-core datasets, many functions support Dask arrays (experimental):
uv pip install "scanpy[leiden]" dask
See the Using dask with Scanpy tutorial. For GPU-accelerated scanpy-like operations, use rapids-singlecell as a separate package.
If the input is an R-native single-cell object (.rds, .RData, Seurat, or SingleCellExperiment), first convert it to .h5ad with R tooling, then load it with Scanpy. Read references/r_interop.md for agent-run installation and conversion instructions across macOS, Linux, and Windows.
For AnnData structure and I/O details, use the anndata skill. For probabilistic models and batch correction, use scvi-tools.
When to Use This Skill
This skill should be used when:
- Analyzing single-cell RNA-seq data (.h5ad, 10X, CSV formats)
- Working with R-friendly single-cell datasets (
.rds,.RData, Seurat, SingleCellExperiment) that need conversion to.h5ad - Performing quality control on scRNA-seq datasets
- Creating UMAP, t-SNE, or PCA visualizations
- Identifying cell clusters and finding marker genes
- Annotating cell types based on gene expression
- Conducting trajectory inference or pseudotime analysis
- Generating publication-quality single-cell plots
What ships with it
24 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.
- assets/analysis_template.py 9.6 KB runs code
- assets/celltype_mapping.json 184 B
- assets/gene_signatures.json 355 B
- assets/pipeline_config.json 380 B
- references/analysis_workflow.md 6.5 KB
- references/api_reference.md 8.2 KB
- references/plotting_guide.md 9.9 KB
- references/r_interop.md 11 KB
- references/standard_workflow.md 6.0 KB
- scripts/_common.py 4.4 KB runs code
- scripts/annotate.py 3.5 KB runs code
- scripts/batch_correct.py 2.7 KB runs code
- scripts/cluster.py 2.5 KB runs code
- scripts/convert.py 1.5 KB runs code
- scripts/find_markers.py 3.4 KB runs code
- scripts/inspect_data.py 2.8 KB runs code
- scripts/plot.py 3.5 KB runs code
- scripts/preprocess.py 3.7 KB runs code
- scripts/pseudobulk.py 2.9 KB runs code
- scripts/qc_analysis.py 4.5 KB runs code
- scripts/reduce_dimensions.py 2.6 KB runs code
- scripts/run_pipeline.py 7.9 KB runs code
- scripts/score_genes.py 3.7 KB runs code
- scripts/subset.py 2.5 KB runs code
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.
- 1mo ago First seen · 321 lines · 93 tokens per session scan A aad13ea7d74d
scanpy is a skill published in the GitHub repository agentlas-ai/agentlas-desktop (6 stars, last pushed yesterday), licensed Apache-2.0. It adds 93 tokens to every session and 4,178 once invoked, about $0.0004 per session on Opus 5.5. A static security scan graded it A with 0 findings. It is 100% identical to scanpy, differing in 66 lines, and is treated as a copy.
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