Usage

InSituCNV is designed to be used both as a Python package and through provided notebooks. Install the package into the Python environment that runs your notebooks, then import it directly with no sys.path changes.

Python API

You can import InSituCNV in your Python scripts or notebooks:

import insitucnv as icv

# Example: smooth data for CNV inference
icv.tl.smooth_data_for_cnv(adata)

# Example: run inferCNV
icv.tl.run_infercnv(adata, reference_key='cell_type', reference_categories=['Stromal'])

For more detailed information, see the Tutorials section.