> ## Documentation Index
> Fetch the complete documentation index at: https://kalarislabs.com/llms.txt
> Use this file to discover all available pages before exploring further.

# cellxgene-census — AI agent skill for scientific databases

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

# `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.

**Category:** [scientific-databases](/skills#scientific-databases) · **License:** MIT · **Version:** 1.3

## Install

```bash theme={null}
npx research-agent-skills install cellxgene-census
npx skills add KalarisLabs/research-agent-skills --skill cellxgene-census
```

## When to use it

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.

## Full playbook

Read [SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/main/skills/cellxgene-census/SKILL.md) for the complete workflow, references and any scripts. The agent installer copies the full skill folder.