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

Ready to run

npx skills add https://github.com/nahisaho/satori --skill scientific-cellxgene-census

💬 Prompt for ChatGPT / Claude Chat▼

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.