Individual skill
cellxgene-census
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.
skills/cellxgene-census/SKILL.md
Source commit 2d2065fb4520fa3f3f2bcf61cff26ec8b7eba4b5
What was checked
- Matches the observed repository HEAD
- Yes
- Scanner rules are current
- Yes
- Repository scan complete
- No
- Skill scan complete
- No
- Observed behavior
- Network or broad shell
- Last checked
- Nov 10, 2026
These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.
Install this skill
Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.
An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.
Repository context
- Repository stars (not skill ratings)
- 56,821
- Repository last updated
- Nov 9, 2026
- License
- MIT
Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.
- ai-scientist Repository topic
- bioinformatics Repository topic
- chemoinformatics Repository topic
- claude Repository topic
- claude-skills Repository topic
- claudecode Repository topic
- clinical-research Repository topic
- computational-biology Repository topic
- data-analysis Repository topic
- drug-discovery Repository topic
- data Derived category
Files and excerpt
File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.
Browse files
SKILL.mdcore · 13,648 bytesSKILL.mdcore · 13,648 bytesSKILL.mdcore · 13,648 bytesSKILL.mdcore · 13,648 bytesSKILL.mdcore · 13,648 bytesSKILL.mdcore · 13,648 bytesSKILL.mdcore · 13,648 bytesSKILL.mdcore · 13,648 bytesSKILL.mdcore · 13,648 bytesSKILL.mdcore · 13,648 bytesSKILL.mdcore · 13,648 bytesSKILL.mdcore · 13,648 bytesSKILL.mdcore · 13,648 bytesSKILL.mdcore · 13,648 bytesSKILL.mdcore · 13,648 bytesSKILL.mdcore · 13,648 bytesSKILL.mdcore · 13,648 bytesreferences/api_access.mddoc · 5,917 bytesreferences/census_schema.mddoc · 9,491 bytesreferences/common_patterns.mddoc · 15,522 bytesreferences/core_workflow_patterns.mddoc · 10,990 bytes
Read excerpt
# 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**