Agent skill · research science · aiskillstore
cellxgene-census
Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools.
Why this skill is useful
Provides specific commands and workflows for querying and analyzing large-scale single-cell genomics data that the AI wouldn't reliably generate on its own.
What it needs
Requires cellxgene-census installed locally. About 7k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
CZ CELLxGENE Census Overview The CZ CELLxGENE Census provides programmatic access to a comprehensive, versioned collection of standardized single-cell genomics data from CZ CELLxGENE Discover. This skill enables efficient querying and analysis of millions of cells across thousands of datasets. The Census includes: 61+ million cells from human and mouse Standardized metadata (cell types, tissues, diseases, donors) Raw gene expression matrices Pre-calculated embeddings and statistics Integration with PyTorch, scanpy, and other analysis tools When to Use This Skill This skill should be used when: Querying single-cell expression data by cell type, tissue, or disease Exploring available single-cell datasets and metadata Training machine learning models on single-cell data Performing large-scale cross-dataset analyses Integrating Census data with scanpy or other analysis frameworks Computing statistics across millions of cells Accessing pre-calculated embeddings or model predictions Installation and Setup Install the Census API: For machine learning workflows, install additional dependencies: Core Workflow Patterns 1. Opening the Census Always use the context manager to ensure proper resource cleanup: Key points: Use context manager (with statement) for automatic cleanup Specify censusversion for reproducible analyses Default opens latest "stable" release 2. Exploring Census Information Before querying expression data, explore available datasets and metadata. Access summary information: Query cell metadata to understand available data: Important: Always filter for isprimarydata == True to avoid counting duplicate cells unless specifically analyzing duplicates. 3. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/cellxgene-census--5d08da