AI Workspace User Guide
Last Updated: January 15, 2026
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
- Co-Embed Workflow - Integration of multiple datasets
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
Sunset: The AI Workspace will be retired on January 11, 2027, and no further updates are planned. Log in before that date to download any datasets you want to keep.
This documentation reflects the final version of the AI Workspace, which will be retired on January 11, 2027.