AI导哈

数据与研究

cellxgene-census

k-dense-ai/scie…t-skills

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.

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安装命令

npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill cellxgene-census

SKILL.md

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.

The Census includes:

  • 217+ million total cells and 125+ million unique cells in the 2025-11-08 stable LTS release
  • 1,845 datasets in the 2025-11-08 stable LTS release
  • Human, mouse, marmoset, rhesus macaque, and chimpanzee data in the current schema
  • Standardized metadata (cell types, tissues, diseases, donors)
  • Raw gene expression matrices and source H5AD lookup/download helpers
  • Pre-calculated summary counts, embeddings, and spatial data
  • Integration with AnnData, Scanpy, TileDB-SOMA, TileDB-SOMA-ML, and other analysis tools

When to Use This Skill

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