cellxgene-census
Query CELLxGENE Census Data
Single-cell Census queries can be hard to scope, filter, and load efficiently. This skill guides Claude, Codex, and Claude Code through reliable CELLxGENE Census workflows.
Install with my Agent
Copy this request to your Agent. It includes the canonical Skill page and manifest.
Review the Skillstore skill "cellxgene-census" from https://skillstore.io/skills/k-dense-ai-cellxgene-census.md and its manifest at https://skillstore.io/api/skills/k-dense-ai-cellxgene-census/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.Your Agent should still show its plan and request any confirmation required by the security policy.
Agent-readable resources
Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.
Test it
Using "cellxgene-census". Find immune cell types in human lung without loading expression data.
Expected outcome:
The response gives a metadata-only query plan, required columns, a primary-data filter, and a count-by-cell-type summary approach.
Using "cellxgene-census". Compare marker gene expression across lung, liver, and kidney macrophages.
Expected outcome:
The response recommends a focused gene filter, tissue filter, Census version pinning, and Scanpy-ready AnnData handling.
Using "cellxgene-census". Train a model on all primary human Census cells.
Expected outcome:
The response recommends a dataloader-based workflow, batch processing, label selection, validation splits, and resource checks.
Security Audit
SafeAll static findings were reviewed against the cited files and adjudicated as false positives. The alerts come from Markdown fences, inline code, Python CELLxGENE examples, or filter syntax rather than command execution or system reconnaissance. No prompt injection, data exfiltration intent, or other semantic security issue was found.
Risk Factors
⚙️ External commands (77)
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<iframe src="https://skillstore.io/embed/skills/k-dense-ai-cellxgene-census.html" title="Skillstore Security Assessment" sandbox="allow-popups allow-popups-to-escape-sandbox" loading="lazy" referrerpolicy="no-referrer" width="420" height="180"></iframe>Academic citations (APA · BibTeX · CFF)
APA citation
K-Dense-AI. (2026). cellxgene-census security audit report (audit version 8) [Author version unspecified]. Skillstore. https://skillstore.io/skills/k-dense-ai-cellxgene-census/audits/8BibTeX citation
@techreport{k-dense-ai-k-dense-ai-cellxgene-census-2026,
author = {K-Dense-AI},
title = {cellxgene-census security audit report (audit version 8)},
institution = {Skillstore},
year = {2026},
number = {8},
url = {https://skillstore.io/skills/k-dense-ai-cellxgene-census/audits/8},
note = {Author version unspecified}
}CITATION.cff
cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "cellxgene-census security audit report (audit version 8)"
version: "unspecified"
type: report
authors:
- name: "K-Dense-AI"
date-released: "2026-07-06"
url: "https://skillstore.io/skills/k-dense-ai-cellxgene-census/audits/8"
identifiers:
- type: other
value: "skillstore:k-dense-ai-cellxgene-census:audit:8"
description: "Skillstore immutable audit report identifier"
Compare variants
2 installable variantsEach author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.
Why this variant is first
davila7-cellxgene-census
2026-09-09
k-dense-ai-cellxgene-census
2026-09-09
Skillstore Score
Why this score Evidence Confidence: HighWhat You Can Build
Explore cell populations
Find available cell types, tissues, diseases, and donor metadata before loading expression matrices.
Build reference datasets
Create focused AnnData objects for marker genes, tissues, diseases, or cross-dataset comparisons.
Train Census-based models
Plan PyTorch dataloaders and train-test splits for large single-cell learning tasks.
Try These Prompts
Use the cellxgene-census skill to list available human lung cell types. Include the primary-data filter and needed columns.
Use the cellxgene-census skill to plan an AnnData query for CD4, CD8A, and CD19 in human T and B cells.
Use the cellxgene-census skill to design an out-of-core brain tissue query and explain how to estimate query size first.
Use the cellxgene-census skill to outline a PyTorch workflow for training a cell type classifier from Census data.
Best Practices
- Always include is_primary_data when duplicate cells would bias the analysis.
- Pin a Census version when results must be reproducible.
- Use metadata queries to estimate size before loading expression matrices.
Avoid
- Loading broad expression matrices before checking available cell counts.
- Mixing Census versions within one analysis without documenting the difference.
- Querying marker genes without checking dataset presence or gene identifiers.
Frequently Asked Questions
What does this skill help me do?
Does it download Census data by itself?
Can it help with very large queries?
Can I use it with Scanpy?
Can it support machine learning workflows?
Should I use it for my own private data?
Developer Details
Author
K-Dense-AILicense
Unknown
Skillstore revision
r1
Version notice
The author did not declare a version.
Repository
https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/cellxgene-censusRef
b8ca75d2c0a7e7102978993058777d82b8ab2610
Maintenance freshness
7/18/2026
Usage
7 downloads · 203 views
File structure