Cellxgene Census

Cellxgene Census is a Data skill for Claude Code, published by K-Dense-AI in scientific-agent-skills.

33.5K stars3.3K forkson K-Dense-AI/scientific-agent-skillsAdded 2026/08/14Repository updated 2026/08/13

agent-skillsai-scientistbioinformaticschemoinformaticsclaudeclaude-skillsclaudecodeclinical-researchcomputational-biologydata-analysisdrug-discoverygenomicsmaterials-sciencemetabolomicsproteomicsscientific-computingscientific-visualization

Install in seconds

Install Cellxgene Census

Copy Cellxgene Census into your Claude Code skills folder. Run the command in your terminal, or review the source on GitHub before installing.

terminal

npx degit https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cellxgene-census ~/.claude/skills/cellxgene-census

Requires Node.js. Downloads this skill only — not the rest of the repository — into your Claude Code skills folder.

Without Node.js

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git

Clones the whole repository, then copy the skill’s own directory into your skills folder yourself.

In this catalog

Source file: skills/cellxgene-census/SKILL.md in K-Dense-AI/scientific-agent-skills
Installs to: ~/.claude/skills/cellxgene-census
Collection: One of 25 skills cataloged from this repository
Category: Data — 668 skills

What Cellxgene Census does

Cellxgene Census queries the CZ CELLxGENE Census programmatically for versioned single-cell and spatial transcriptomics data, including metadata, gene expression, summary counts, embeddings, and source H5AD files. Use it for large-scale bioinformatics analyses, machine learning on cell data, or cross-dataset comparisons.

Cellxgene Census is cataloged under Data on DirSkills. Cellxgene Census comes from a repository tagged agent-skills, ai-scientist, bioinformatics, chemoinformatics and claude.

Documentation

README

Excerpt

CZ CELLxGENE Census

Overview

The CZ CELLxGENE Census provides programmatic access to a comprehensive, versioned collection of standardized single-cell and spatial transcriptomics data from CZ CELLxGENE Discover. This skill enables efficient querying and analysis of public Census releases without downloading whole datasets first.

This is the opening of the README. Read the full README on GitHub.

Frequently asked about Cellxgene Census

What else does K-Dense-AI publish alongside Cellxgene Census?
Cellxgene Census is one of 25 skills that DirSkills catalogs from K-Dense-AI/scientific-agent-skills, the repository it ships in. Its siblings there include Adaptyv Bio Foundry API, Aeon and Analytical Method Validation. Each one is a separate skill with its own page in this directory, installs the same way Cellxgene Census does, and is maintained by K-Dense-AI in that same repository. The rest of the collection is listed on the K-Dense-AI/scientific-agent-skills page.
How does Cellxgene Census compare to other Data skills?
Cellxgene Census ranks #43 by stars among the 668 Data skills in this catalog. The most-starred ones next to it are Benchmark Methodology, Jupyter Notebook and Solana. DirSkills ranks by the star count of the repository each skill ships in, so that order reflects how popular those repositories are rather than any review of Cellxgene Census against them. Open each page to compare what they document and how they install.