Individual skill
cellxgene-census
Query 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.
plugins/KalarisLabs/research-agent-skills/skills/cellxgene-census/SKILL.md
Source commit d780783eba4ecc7c8b9429f95c9362df95f07c61
What was checked
- Matches the observed repository HEAD
- Yes
- Scanner rules are current
- No
- Repository scan complete
- No
- Skill scan complete
- No
- Observed behavior
- Not checked yet
- Last checked
- Nov 4, 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)
- 1,537
- Repository last updated
- Nov 7, 2026
- License
- Apache-2.0
Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.
- ai-coding Repository topic
- awesome Repository topic
- awesome-list Repository topic
- codex Repository topic
- codex-plugins Repository topic
- openai Repository topic
- codex-skill Repository topic
- codex-skills Repository topic
- marketplace Repository topic
- codex-marketplace Repository topic
- data Derived category
Declared tags are partial or unavailable.
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 · 12,636 bytesSKILL.mdcore · 12,636 bytesSKILL.mdcore · 12,636 bytesSKILL.mdcore · 12,636 bytesSKILL.mdcore · 12,636 bytesSKILL.mdcore · 12,636 bytesSKILL.mdcore · 12,636 bytesSKILL.mdcore · 12,636 bytesSKILL.mdcore · 12,636 bytesSKILL.mdcore · 12,636 bytesSKILL.mdcore · 12,636 bytesSKILL.mdcore · 12,636 bytesSKILL.mdcore · 12,636 bytesSKILL.mdcore · 12,636 bytesSKILL.mdcore · 12,636 bytesSKILL.mdcore · 12,636 bytesSKILL.mdcore · 12,636 bytesreferences/census_schema.mddoc · 7,910 bytesreferences/common_patterns.mddoc · 11,033 bytesreferences/core_workflow_patterns.mddoc · 9,796 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**