Command Line Interface

stangene provides a CLI via python -m stangene or the stangene command (if installed via pip).

harmonize

Harmonize gene identifiers in a dataset.

stangene harmonize --input <file> --species <species> --output-dir <dir> [options]

Argument	Required	Description
--input	Yes	Path to input file (.h5ad, .tsv, .csv)
--species	Yes	Species name (human or mouse)
--output-dir	Yes	Directory to write output files
--dataset-name	No	Optional dataset label (defaults to filename)
--reference-dir	No	Custom reference directory

Example:

stangene harmonize \
    --input data/pbmc3k.h5ad \
    --species human \
    --output-dir results/pbmc3k/ \
    --dataset-name pbmc3k

build-refs

Build reference annotation databases for a species.

stangene build-refs --species <species> [options]

Argument	Required	Description
--species	Yes	Species name (human or mouse)
--reference-dir	No	Custom reference directory
--force	No	Force re-download and rebuild

Examples:

# First-time build
stangene build-refs --species human
stangene build-refs --species mouse

# Update to latest references
stangene build-refs --species human --force