Overview
Immunology workflows support immune state discovery, repertoire diversity, cytokine signaling, disease cohort comparison, and multi-modal immune profiling.
Use case index
| Use case | Research question | Key capabilities |
|---|---|---|
| Immune atlas and annotation | Which immune populations and states are present? | Annotation, state scoring, composition |
| Repertoire diversity | Which clones are expanded or shared across samples? | TCR/BCR clonotypes, diversity, overlap |
| Cytokine signaling | Which ligand-receptor and cytokine pathways dominate? | Communication, cytokine networks, pathway deltas |
| Ligand-to-target hypotheses | Which sender ligands may explain receiver target-gene programs? | Ligand activity ranking, target genes, ligand-receptor-target paths |
| Spatial immune neighborhoods | Which spatial neighborhoods, TLS-like regions, and cytokine gradients organize immune tissue biology? | Graph neighborhoods, enrichment, TLS criteria, cytokine gradients |
| Disease cohort comparison | How do immune profiles vary across disease contexts? | Cohort metadata, composition, trajectory, spatial patterns |
| Multi-modal profiling | How do protein, ATAC, and cytometry measurements support immune phenotypes? | CITE-seq, ATAC, multiome, cytometry |
Common starting data
- per-cell annotations
- scRNA-seq or CITE-seq tables
- VDJ contig/AIRR/bulk repertoire tables
- spatial cell coordinate tables
- cohort metadata
- ATAC peak tables
- cytometry event tables
Research-only scope
These use cases support exploratory and translational research. They are not clinical diagnostic workflows.