How do I filter for specific cell types?

Use the obs_value_filter parameter within querying functions (like get_anndata) to specify criteria such as cell_type == 'B cell'.

Can this handle datasets larger than my available RAM?

Yes, for queries exceeding RAM, use the axis_query() method to process the expression matrix in chunks using iterative batches.

How do I ensure my genomics analysis is reproducible?

You should always specify a specific census_version (e.g., '2023-07-25') when opening the SOMA object to ensure consistent data results over time.

Does it support both human and mouse data?

Yes, the Census provides programmatic access to standardized data for both Homo sapiens and Mus musculus.

CZ CELLxGENE Census

Name: CZ CELLxGENE Census
Author: K-Dense-AI

byK-Dense-AI

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3,717

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Data Science & ML

Provides programmatic access to standardized single-cell genomics data for high-scale querying, analysis, and machine learning integration.

This skill empowers researchers and bioinformaticians to query over 61 million cells from the CZ CELLxGENE Census directly within Claude. It streamlines the process of filtering high-dimensional genomics data by cell type, tissue, or disease, facilitating seamless integration with popular analysis frameworks like Scanpy and PyTorch. Whether you are performing population-scale analysis, training machine learning models, or exploring cross-dataset metadata, this skill handles everything from resource-efficient data loading to out-of-core processing for massive datasets.

Key Features

01Programmatic access to 61M+ single-cell genomics records

02Direct integration with Scanpy and PyTorch workflows

03Standardized metadata filtering by cell type, tissue, and disease

04Out-of-core processing for large-scale dataset queries

05Reproducible data access via versioned Census releases

063,717 GitHub stars

Use Cases

01Automated metadata exploration and cell type distribution reporting

02Training machine learning models on human and mouse cell data

03Large-scale cross-dataset single-cell expression analysis

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add k-dense-ai/claude-scientific-skills cellxgene-census

For use in Claude.ai and ChatGPT

Download Skill