Description
cellxgene-census is an agent skill for querying the CZ CELLxGENE Census, a versioned collection of standardised single-cell and spatial transcriptomics data from CZ CELLxGENE Discover. It is for population-scale analysis of public data, and it lets you query the public Census releases without downloading whole datasets first. The skill describes the stable LTS release from 8 November 2025, which contains more than 217 million cells, more than 125 million unique cells and 1,845 datasets. It covers human, mouse, marmoset, rhesus macaque and chimpanzee data in the current schema. The Census includes standardised metadata for cell types, tissues, diseases and donors, raw gene expression matrices, source H5AD lookup and download helpers, pre-calculated summary counts, embeddings and spatial data. It works with AnnData, Scanpy, TileDB-SOMA and TileDB-SOMA-ML. Use it when you need to pull a subset of public single-cell data across many studies. The skill is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars. The listing shows it as free, and it has about 1,800 installs.…
Highlights
- Queries versioned public single-cell data
- Query without downloading whole datasets
- Standardised cell type, tissue, disease and donor metadata
- Covers five species in the current schema
- Works with AnnData, Scanpy and TileDB-SOMA
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cellxgene-census FAQ
What is the Census?
A versioned collection of standardised single-cell and spatial transcriptomics data from CZ CELLxGENE Discover.
How much data is in it?
The skill describes the 8 November 2025 stable LTS release as having more than 217 million cells and 1,845 datasets.
Which species are covered?
Human, mouse, marmoset, rhesus macaque and chimpanzee data in the current schema.
Does it need full downloads?
No. The skill is built to query public releases without downloading whole datasets first.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill cellxgene-census.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best cellxgene-census alternatives?
Popular alternatives to cellxgene-census include anndata, arboreto and imaging-data-commons. See all cellxgene-census alternatives