References
==========

InSituCNV builds upon several excellent packages in the single-cell and spatial transcriptomics ecosystem.

* **infercnvpy**: We use `infercnvpy <https://infercnvpy.readthedocs.io/>`_ for the core CNV inference logic.
* **scVelo**: Smoothing and other transcriptomic analysis steps utilize `scVelo <https://scvelo.readthedocs.io/>`_.
* **Scanpy**: General single-cell analysis is powered by `Scanpy <https://scanpy.readthedocs.io/>`_.
* **AnnData**: Data structures are based on `AnnData <https://anndata.readthedocs.io/>`_.

Publications
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If you use InSituCNV in your research, please cite:

* Jensen et al., *In Situ* Inference of Copy Number Variations in Image-Based Spatial Transcriptomics (2024).