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scientific-human-cell-atlas

Search HCA Data Portal projects and export CELLxGENE Census subsets for Scanpy analysis.

3|1|Updated Feb 11, 2026
Search Tags:#single-cell#cellxgene#data-portal#file-download#project-search#hca
One-click install
npx skills add https://github.com/nahisaho/satori --skill scientific-human-cell-atlas
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: scientific-human-cell-atlas
Source: https://github.com/nahisaho/satori/tree/main/src/.github/skills/scientific-human-cell-atlas
Command: npx skills add https://github.com/nahisaho/satori --skill scientific-human-cell-atlas

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Access to comprehensive Human Cell Atlas (HCA) data and CELLxGENE Census resources is scattered across portals, making it hard for researchers to locate relevant projects, retrieve files, and perform cross-dataset cell-type analyses.

Core Features & Use Cases

  • Discover HCA Data Portal projects and related metadata (organ, disease, library method) through unified search.
  • Query CELLxGENE Census to access large-scale single-cell atlases, filter by tissue and disease, and export ready-to-analyze data.
  • Orchestrate end-to-end atlas workflows: from project search to data retrieval, preprocessing, and cell-type composition analysis.

Quick Start

Run an HCA atlas pipeline to search projects for a given organ and disease, download files, query CELLxGENE Census, and perform a cell-type composition analysis.

Frequently Asked Questions about scientific-human-cell-atlas

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I find Human Cell Atlas projects for a specific organ and disease?▼

You can search the Human Cell Atlas (HCA) Data Portal by filtering matching metadata for specific organs, diseases, and library methods to locate relevant single-cell projects for your research.

How do I export filtered single-cell atlas data for downstream Scanpy analysis?▼

You can query the CELLxGENE Census to filter large-scale single-cell atlases by tissue and disease, then export a ready-to-analyze subset directly to your project directory for downstream Scanpy processing.

Can I orchestrate an end-to-end single-cell workflow from project search to cell-type composition analysis?▼

Yes, you can orchestrate end-to-end atlas workflows that span from HCA project search and file download to CELLxGENE Census querying, data retrieval, preprocessing, and final cell-type composition analysis.

What is the best way to query the CELLxGENE Census for tissue-specific single-cell data?▼

The best way to query the CELLxGENE Census for tissue-specific single-cell data is to use unified search parameters to filter large-scale atlases by organ, tissue, and disease metadata before exporting.

Do I need a specific project directory setup to download HCA data and CELLxGENE Census exports?▼

Yes, you need to ensure query results and exported data subsets are saved to a designated project directory so they remain organized and ready for downstream processing with Scanpy.

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