celltypist-cell-annotation - Annotate scRNA-seq cells with CellTypist
Annotates normalized scRNA-seq AnnData with pre-trained CellTypist models and returns per-cell labels, cluster consensus labels, and confidence scores.
Tags
Updated: 2026-10-04Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Annotate cells automatically
- Assign cluster consensus labels
- Report confidence scores
- Download reference models
- Train custom models
- Visualize annotation results
Inputs
- Normalized AnnData object
- CellTypist model
- Cluster assignments
Outputs
- Annotated AnnData object
- Per-cell labels
- Cluster consensus labels
- Confidence scores
- Annotation visualization file
Requirements
- Python 3.8 or later
- celltypist 1.6 or later
- scanpy 1.9 or later
- anndata package
- 8 GB RAM
- Internet access for model downloads