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 AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-anndatagit clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-SkillsWrote 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/alterlab-ieu/alterlab-academic-skills/alterlab-anndata)<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-anndata"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-anndata/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/alterlab-ieu/alterlab-academic-skills/alterlab-anndata"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-anndata.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 1 finding, up to high
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 →
- high Anti-Refusal · line 83 Skill instructs the agent to omit warnings, disclaimers, or ethical commentary. Stripping safety caveats hides risk from the user and is a common jailbreak preamble.Fix: Remove instructions that suppress warnings, disclaimers, or ethical commentary. Let the agent surface safety-relevant caveats to the user.
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 | $0.00133 | $0.03846 |
| Opus 5.5 | $0.00053 | $0.01538 |
| Sonnet 5.5 | $0.00027 | $0.00769 |
| Haiku 4.5 | $0.00013 | $0.00385 |
Grade A, and why
alterlab-anndata 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.
How it starts
The opening of the file, as written. The whole thing — 422 lines — stays where its author put it; the contents beside it link to each section on GitHub.
AnnData
Overview
AnnData is a Python package for handling annotated data matrices, storing experimental measurements (X) alongside observation metadata (obs), variable metadata (var), and multi-dimensional annotations (obsm, varm, obsp, varp, uns). Originally designed for single-cell genomics through Scanpy, it now serves as a general-purpose framework for any annotated data requiring efficient storage, manipulation, and analysis.
When to Use This Skill
Use this skill when:
- Creating, reading, or writing AnnData objects
- Working with h5ad, zarr, or other genomics data formats
- Performing single-cell RNA-seq analysis
- Managing large datasets with sparse matrices or backed mode
- Concatenating multiple datasets or experimental batches
- Subsetting, filtering, or transforming annotated data
- Integrating with scanpy, scvi-tools, or other scverse ecosystem tools
Does NOT Trigger
| Scenario | Use Instead |
|---|---|
| QC, normalization, HVG, clustering, UMAP, or marker genes | alterlab-scanpy |
| RNA velocity from spliced/unspliced layers | alterlab-scvelo |
| Deep generative models / batch integration (scVI, scANVI) | alterlab-scvi-tools |
| Querying the public CELLxGENE Census for reference cells | alterlab-cellxgene |
| Chunked n-dimensional arrays outside the AnnData model | alterlab-zarr |
Installation
uv pip install anndata # 0.13.x as of 2026-09; needs Python >= 3.12
# Lazy/backed reads (ad.experimental.read_lazy) need dask + xarray:
uv pip install 'anndata[lazy]' # or 'anndata[dask]' for dask-backed arrays only
What changed in 0.13 (breaking)
These bite existing scripts, so check them before running older code:
AnnData.concatenate()is gone — use the module-levelad.concat([...])..Xis copy-on-write likelayers/obsm: writing into a subset (view.X = 0) no longer propagates to the parent object..Xis now stored aslayers[None], so it shows up in the repr and in.layers.keys().- The
dtype=argument to theAnnDataconstructor was removed — castXyourself. - zarr v3 only (
zarr >= 3.1); writing the v2 format is deprecated as of 0.13.4 and goes away in 0.14. Stores are written sharded by default. anndata.__version__and theadata.*_keys()methods are deprecated — useimportlib.metadata.version("anndata")andsorted(adata.obs)/k in adata.uns.- Loom I/O is deprecated (
ad.io.read_loom,adata.write_loom) in favour of h5ad/zarr.
What ships with it
6 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.
- 1mo ago Changed · +25 lines f923eb4ecdec
- 1mo ago First seen · 397 lines · 133 tokens per session scan A 04f076625984
alterlab-anndata is a skill published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (78 stars, last pushed 3d ago), licensed MIT. It adds 133 tokens to every session and 3,846 once invoked, about $0.0005 per session on Opus 5.5. 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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