Annotation and state scoring
The immune_annotation pipeline labels immune cells and scores immune state programs.
Outputs
| Output | Description |
|---|---|
labels | Immune hierarchy label counts and proportions |
groups | Group-level label summaries |
state_programs | Mean scores for immune gene programs |
cells_preview | Per-cell preview with broad label, immune label, confidence, and state scores |
run_record | Gene set source, annotation parameters, and CellTypist model field |
Built-in programs
- exhaustion
- activation
- effector function
- cytotoxicity
- regulatory suppression
CellTypist gate
The pipeline detects whether CellTypist is available, but concrete model execution requires a configured model asset. Until then, celltypist_model_version is logged as null.
Interpretation
AI summaries cite computed labels and state scores only. They do not infer clinical immune status or treatment response.