cellxgene-census SKILL.md skillA
cellxgene-census from k-dense-ai/scientific-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add k-dense-ai/scientific-agent-skills/cellxgene-census@v1.5Pins v1.5 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- k-dense-ai/scientific-agent-skills
- Path
skills/cellxgene-census/SKILL.md- Versions recorded
- 6
- Latest version
- v1.5, committed Oct 1, 2026
- First version recorded
- Jun 11, 2026
- Size
- 13,648 bytes
- Repository stars
- 53,159
- License
- MIT
Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# CZ CELLxGENE Census ## Overview The CZ CELLxGENE Census provides programmatic access to a comprehensive, versioned collection of standardized single-cell and spatial transcriptomics data from CZ CELLxGENE Discover. This skill enables efficient querying and analysis of public Census releases without downloading whole datasets first. The Census includes: - **217+ million total cells** and **125+ million unique cells** in the 2025-11-08 stable LTS release - **1,845 datasets** in the 2025-11-08 stable LTS release - **Human, mouse, marmoset, rhesus macaque, and chimpanzee** data in the current schema - **Standardized metadata** (cell types, tissues, diseases, donors) - **Raw gene expression** matrices and source H5AD lookup/download helpers - **Pre-calculated summary counts, embeddings, and spatial data** - **Integration with AnnData, Scanpy, TileDB-SOMA, TileDB-SOMA-ML, and other analysis tools** ## When to Use This Skill This skill should be used when: - Querying single-cell expression data by cell type, tissue, or disease - Exploring available single-cell datasets and metadata - Training machine learning models on single-cell data …
Read the whole file at its exact version.
How to install
mdr add k-dense-ai/scientific-agent-skills/cellxgene-census@sha256:123b66d6701c7c05The line at the top of this page pins the label v1.5, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_g2xcdhqeojgyhbn2)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 6 versions of this file, between Jun 11, 2026 and Oct 1, 2026, about one every 22 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v1.5 latest | 2026-10-01 | a92663a | 13,648 B | A | view · diff |
| v1.4 | 2026-09-30 | ce9e6e9 | 12,342 B | A | view · diff |
| v1.3 | 2026-09-02 | 1e5eeff | 11,393 B | A | view · diff |
| v1.2 | 2026-07-26 | 2f2022d | 10,435 B | A | view · diff |
| v1.1 | 2026-07-26 | b085e11 | 19,132 B | A | view · diff |
| git:20260611.1b8fae3 | 2026-06-11 | 1b8fae3 | 19,137 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (13648 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
k-dense-ai/scientific-agent-skills · 53,159 stars · license MIT · pushed 2026-10-19 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_g2xcdhqeojgyhbn2 GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/cellxgene-census GET https://markdownregistry.com/api/v1/blob/123b66d6701c7c0587d0a615a2394caee52e62745b3fd31176381ea64aaa794a
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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