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CZ CELLxGENE Census · lingxling | DecimalAI

scienceby lingxling

CZ CELLxGENE Census

lingxling/cellxgene-census

Source lingxling/awesome-skills-cn ↗License MIT

Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data.

SkillScore100Maintained

Automatic

Research pack

Last verified 8/28/2026

What it changes

Passed 22 of 22 test cases with the skill, and 11 of 22 without it.

Without skill50%

With skill100%

Checks it passed that the model alone missed

Passes census_version="2025-11-08" to open_soma
Uses cellxgene_census.get_obs to query cell metadata
Specifies the package extra cellxgene-census[spatial]

and 12 more in the full report

11 fixed11 passed either way0 still failing0 broke

Pass-rate lift: +50 pp
Tokens: +159%
Agent turns: 0%
Response time: -50%

Model gemini-3.6-flashMeasured 8/28/2026v122 of 22 cases passed with skill

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/lingxling-cellxgene-census/SKILL.md https://app.decimal.ai/s/lingxling-cellxgene-census/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add lingxling-cellxgene-census, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/lingxling-cellxgene-census/ and pins it in .decimal/skills.lock

decimalai skills add lingxling-cellxgene-census

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/lingxling-cellxgene-census/SKILL.md https://app.decimal.ai/s/lingxling-cellxgene-census/SKILL.md

Raw file: /s/lingxling-cellxgene-census/SKILL.md ↗ · machine-readable summary at /s/lingxling-cellxgene-census.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 11 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 11

Prompt

What exact pip package installation command should I run to install cellxgene-census with all necessary dependencies for spatial transcriptomics workflows?

What was checked, without and with the skill
Checked	Without skill	With skill
Specifies the package extra cellxgene-census[spatial]	Missed	Passed
Includes spatialdata in the installation requirement	Passed	Passed

case-16 · gemini-3.6-flash · 8/28/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md549 lines3 files

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
Performing large-scale cross-dataset analyses
Integrating Census data with scanpy or other analysis frameworks
Computing statistics across millions of cells
Accessing pre-calculated embeddings or model predictions

Installation and Setup

Install the Census API:

uv pip install "cellxgene-census==1.17.*"

For spatial workflows:

uv pip install "cellxgene-census[spatial]==1.17.*" "spatialdata[extra]>=0.2.5"

For PyTorch model training, use TileDB-SOMA-ML. The old cellxgene_census.experimental.ml loaders are deprecated:

Track record

Benchmark

22 / 22

test cases passed, vs 11 / 22 without

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/3/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

lingxling / awesome-skills-cn

claude-scientific-skills/skills/cellxgene-census/SKILL.md

View on GitHub ↗

License MITImported 8/3/2026Version v1Bundled 2 files

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See it in action

What's inside

CZ CELLxGENE Census

Overview

When to Use This Skill

Installation and Setup

Track record

Benchmark

Adoption

SkillSafety

Source

Other skills for the same job

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