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scientific-cellxgene-census

Query CELLxGENE Census API for dataset metadata and gene expression.

3|1|Updated Feb 11, 2026
Search Tags:#python#metadata#single-cell#data-integration#cellxgene#census#gene-expression
One-click install
npx skills add https://github.com/nahisaho/satori --skill scientific-cellxgene-census
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: scientific-cellxgene-census
Source: https://github.com/nahisaho/satori/tree/main/src/.github/skills/scientific-cellxgene-census
Command: npx skills add https://github.com/nahisaho/satori --skill scientific-cellxgene-census

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

CELLxGENE Census provides scalable access to metadata and gene expression across large single-cell atlases, enabling researchers to fetch cross-atlas datasets efficiently.

Core Features & Use Cases

  • Metadata search across human and mouse census datasets to filter by tissue, disease, and dataset attributes.
  • Gene expression retrieval (adata) for selected genes across atlases, with optional subsetting by cells/datasets.
  • Cross-atlas data integration support by exporting to CSV and AnnData for downstream analyses.

Quick Start

Run a Python script to query CELLxGENE Census for datasets and gene expression with organism and tissue filters.

Frequently Asked Questions about scientific-cellxgene-census

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I query single-cell atlas metadata from the CELLxGENE Census API?▼

To query single-cell metadata from the CELLxGENE Census API, you use the cellxgene_census Python library to filter datasets by tissue and disease, retrieving cell-type distributions and attributes via the census_info endpoint.

How do I retrieve gene expression data across human and mouse single-cell atlases?▼

You retrieve gene expression data across human and mouse single-cell atlases by using the get_anndata function in the cellxgene_census Python library, subsetting results by specific genes, cells, or datasets.

Can I export CELLxGENE Census data to CSV and AnnData formats for downstream analysis?▼

Yes, you can export CELLxGENE Census data to CSV and AnnData formats for downstream analysis. The skill compiles queried metadata and gene expression outputs to support cross-atlas data integration.

Do I need a specific Python environment to access CELLxGENE Census data?▼

Yes, you need a Python environment with the cellxgene_census library installed to access CELLxGENE Census data. This environment is required to utilize functions like get_obs and get_anndata for querying.

What is the best way to filter single-cell gene expression data by tissue and disease?▼

The best way to filter single-cell gene expression data by tissue and disease is to apply these parameters directly within the cellxgene_census API query, compiling structured subsets of human and mouse atlas data.

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