Disease cohort comparison
Use this workflow to compare immune profiles across disease contexts, treatments, timepoints, response labels, and spatial tissue patterns. It connects immune composition, trajectory summaries, graph-based spatial neighborhoods, TLS-like regions, and cohort metadata in one disease-oriented analysis.
Research question
How do immune composition, state trajectories, spatial neighborhoods, and disease metadata vary across disease contexts, treatment groups, or response labels?
Use case
Use this when the study is organized around disease biology rather than a single assay. The workflow is useful for autoimmune, infectious disease, allergy, vaccine, and immunotherapy cohorts where metadata, immune state, spatial context, and cohort comparisons need to be interpreted together.
Supported context fields
- disease label
- disease activity score
- medication
- timepoint
- vaccination or infection history
- treatment condition
- response label
Suggested path
- Register a study with disease context and cohort label.
- Run composition and annotation first.
- Run
disease_workflows. - Review trajectory axis, spatial niches, graph neighborhoods, neighborhood enrichment, TLS-like regions, cytokine/state gradients, region summaries, proximity, and composition comparison.
- Generate report outputs for methods and provenance.
Presets
The workflow includes presets for autoimmune, infectious disease, allergy/atopy, and immunotherapy response contexts.