Immune atlas and annotation

Use this workflow when you need to summarize immune populations and score immune states.

Research questions

• Which immune labels dominate a cohort?
• Are exhaustion, activation, effector, cytotoxicity, or regulatory programs enriched?
• Which labels are available for downstream repertoire, communication, or disease workflows?

Suggested path

1. Register a scrna or cite_seq dataset.
2. Run immune_composition.
3. Run immune_annotation.
4. Review labels and state programs.
5. Generate AI interpretation if completed runs are available.

Outputs to cite

• summary.total_cells
• summary.unique_immune_labels
• label counts
• state program mean scores
• gene set source/version