References

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

• infercnvpy: We use infercnvpy for the core CNV inference logic.

• scVelo: Smoothing and other transcriptomic analysis steps utilize scVelo.

• Scanpy: General single-cell analysis is powered by Scanpy.

• AnnData: Data structures are based on AnnData.

Publications

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).