AI Workspace User Guide
Last Updated: December 14, 2025
Welcome to the AI Workspace! This guide will help you upload, process, and analyze your single-cell RNA sequencing data using computational methods.
What is the AI Workspace?
The AI Workspace allows you to upload your own H5AD files and run sophisticated single-cell analysis workflows, including:
- Dimensionality reduction with PCA, scVI, or TranscriptFormer
- Data comparison with the CELLxGENE Census reference atlas or your own data
- Interactive visualization in CellxGene Explorer
Quickstart
The AI Workspace Quickstart can help you learn how to upload data, run a workflow, and explore embeddings.
Or check out the AI Workspace demo video to see the tool in action.
Further Documentation
Core Concepts
- Data Requirements - H5AD format, organism support, file specifications
- Workflow Types - Standard vs Comparison workflows
- Computational Models - Understanding PCA, scVI, and TranscriptFormer
Workflow Guides
- Standard Workflow - Single-dataset analysis pipeline
- Comparison Workflow - Integration with CELLxGENE Census
Advanced Topics
- Configuration Options - Workflow parameters and settings
- Job Management - Monitoring job status
- Results & Visualization - Understanding outputs
Getting Help
- Tooltips: Hover over question mark icons in the interface for contextual help
- Error Messages: Check workflow errors for specific guidance
- Support: Contact our team for additional assistance
Updates & Changelog
Stay informed about new features, models, and improvements to the AI Workspace.
This documentation is regularly updated to reflect the latest features for single-cell analysis.