Multi-modal profiling

Use this workflow when immune phenotypes are supported by protein, ATAC, cytometry, or multiome data.

Research questions

• Which ADT/protein markers define major immune populations?
• Which accessible peaks and TF motifs are enriched?
• Which cytometry populations are most frequent?
• Which optional dependencies are available for deeper workflows?

Suggested path

1. Register cite_seq, atac, or fcs datasets.
2. Run multimodal_profiling.
3. Review ADT heatmap values, WNN fallback coordinates, ATAC tracks, motif cards, cytometry coordinates, and population bars.
4. Use AI/reporting once completed runs exist.

Dependency gates

• muon for full WNN/multiome graph workflows
• SnapATAC2 for full scATAC preprocessing and peak calling
• FlowUtils or flowutils for binary FCS parsing