Workflows

Overview

The AI Workspace offers two distinct workflow types for analyzing single-cell RNA sequencing data. Each workflow serves different analytical needs and has specific requirements.

Standard Workflow

Analyze your dataset independently without reference to external data.

• Purpose: Single-dataset analysis and exploration
• Data Requirements: H5AD files with ENSEMBL gene IDs
• Available Models: PCA, scVI, TranscriptFormer
• Organism Support: Varies by model (see Data Requirements)

Learn more about Standard Workflow →

Comparison Workflow

Compare your data against the CELLxGENE Census reference atlas.

• Purpose: Contextualize cells against comprehensive reference data
• Data Requirements: H5AD files with human or mouse data only
• Available Models: scVI, TranscriptFormer only
• Gene Requirements: ENSEMBL IDs (ENSG or ENSMUSG prefixes)

Learn more about Comparison Workflow →

Cell Type Classification

Automated cell type annotation available for both workflows when using compatible models and organisms.

• Requirements: scVI or TranscriptFormer models with human or mouse data
• Output: Predicted cell type labels with confidence scores
• Integration: Available as optional configuration in both workflows

Workflow Selection