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 CHENyiru3/AI-Skills-Collections --skill human-cell-atlasgit clone --depth 1 https://github.com/CHENyiru3/AI-Skills-CollectionsWrote 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/chenyiru3/ai-skills-collections/human-cell-atlas)<a href="https://agentmods.dev/skills/chenyiru3/ai-skills-collections/human-cell-atlas"><img src="https://agentmods.dev/badge/skills/chenyiru3/ai-skills-collections/human-cell-atlas/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/chenyiru3/ai-skills-collections/human-cell-atlas"><img src="https://agentmods.dev/badge/skills/chenyiru3/ai-skills-collections/human-cell-atlas.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 | $0.00028 | $0.00475 |
| Opus 5.5 | $0.00011 | $0.00190 |
| Sonnet 5.5 | $0.00006 | $0.00095 |
| Haiku 4.5 | $0.00003 | $0.00047 |
Grade A, and why
human-cell-atlas 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 6d 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
Human Cell Atlas: Reference Atlas
Overview
The Human Cell Atlas (HCA) is a global effort to create a comprehensive reference map of all human cells. The HCA data portal provides access to thousands of single-cell datasets spanning multiple tissues, cell types, and conditions.
When to Use This Skill
This skill should be used when:
- Finding reference single-cell datasets
- Accessing cell type markers and gene expression
- Downloading curated atlases
- Comparing your data to references
- Finding data for specific tissues
Quick Start
Accessing Data
# Using cellxgene-census (for HCA data)
import cellxgene_census
# Get census
census = cellxgene_census.open_soma()
# Query specific tissue
adata = cellxgene_census.get_anndata(
census,
organism="Homo sapiens",
tissue="lung"
)
Direct Download
- Visit https://data.humancellatlas.org/
- Browse projects and datasets
- Download in desired format (h5ad, loom, csv)
Data Portal
Browsing Projects
- Website: https://data.humancellatlas.org/
- Filter by: Tissue, organism, disease, technology
- Metadata: Detailed sample information
Available Data Types
- Single-cell RNA-seq
- Single-cell ATAC-seq
- Spatial transcriptomics
- Multi-omics
Common Uses
Reference Mapping
# Map your data to HCA references
# Use Seurat or scanpy integration
Marker Discovery
# Find markers for cell types
# Query HCA for specific cell types
Additional Resources
- HCA Data Portal: https://data.humancellatlas.org/
- DCP: https://data.humancellatlas.org/explore
- CellxGene Census: https://cellxgene-census.readthedocs.io/
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.
- 6d ago First seen · 86 lines · 28 tokens per session scan A 9b469d299d5b
human-cell-atlas is a skill published in the GitHub repository CHENyiru3/AI-Skills-Collections (1 stars, last pushed 7d ago), licensed MIT. It adds 28 tokens to every session and 475 once invoked, about $0.0001 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 2026-10-02.
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