CLI Overview
Command-line interface for CellType-Refinery.
Installation
The CLI is installed with the package:
pip install -e .
celltype-refinery --help
Commands
| Command | Description |
|---|---|
| preprocess | Run preprocessing stages |
| cluster | Leiden clustering |
| annotate | Marker-based annotation |
| refine | Iterative refinement |
| consolidate | Final consolidation |
| analyze | Composition and spatial |
| pipeline | Full pipeline from config |
Global Options
celltype-refinery --help
celltype-refinery --version
celltype-refinery --verbose COMMAND
celltype-refinery --debug COMMAND