annotate
Run marker-based annotation.
Usage
celltype-refinery annotate [OPTIONS]
Options
| Option | Type | Default | Description |
|---|---|---|---|
--input | PATH | - | Input H5AD file |
--marker-map | PATH | - | Marker map JSON |
--layer | TEXT | batchcorr | Expression layer |
--min-coverage | FLOAT | 0.3 | Minimum coverage |
--min-pos-frac | FLOAT | 0.2 | Minimum positive fraction |
--out | PATH | - | Output directory |