Research · Skill
CZ CELLxGENE Census
Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.
Open in PhởWhat the skill covers
The sections of its instructions, in order.
- 01 Overview
- 02 When to Use This Skill
- 03 Installation and Setup
- 04 Core Workflow Patterns
- 05 Key Concepts and Best Practices
- Always Filter for Primary Data
- Specify Census Version for Reproducibility
- Estimate Query Size Before Loading
- Use tissuegeneral for Broader Groupings
- Select Only Needed Columns
- Check Dataset Presence for Gene-Specific Queries
- Two-Step Workflow: Explore Then Query
- 06 Available Metadata Fields
- Cell Metadata (obs)
- Gene Metadata (var)
- 07 Reference Documentation
- references/censusschema.md
- references/commonpatterns.md
- 08 Common Use Cases
- Use Case 1: Explore Cell Types in a Tissue
Reference files
4 files Phở can open while it uses the skill.
- references/api_access.md
- references/census_schema.md
- references/common_patterns.md
- references/core_workflow_patterns.md
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Frequently asked questions
What does CZ CELLxGENE Census do?
Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.
Is CZ CELLxGENE Census free to use?
Yes. CZ CELLxGENE Census is published by K-Dense under the MIT licence, and you can use it with a free Phở account.
How do I use CZ CELLxGENE Census in Phở?
Press Open in Phở, then Try to apply it to your next message, or add the Scientific Python set so Phở loads it whenever a request matches.
Does CZ CELLxGENE Census need other tools?
No. It works in a normal Phở chat with what you type or upload.
Copied unchanged from K-Dense-AI/claude-scientific-skills at commit a25cf9e and credited to K-Dense, who is not affiliated with Phở. The full instructions and licence text ship with the skill inside Phở.