Feature Request: Integrate inferCNV algorithm

[Aegon8719]

What kind of feature would you like to request?

Additional function parameters / changed functionality / changed defaults?

Please describe your wishes

The inferCNV tool is fundamental for cancer research using scRNA-seq data. It allows researchers to infer large-scale chromosomal copy number variations (CNVs) from gene expression profiles, which is crucial for identifying malignant cells, distinguishing them from normal cells in the tumor microenvironment, and exploring intratumor heterogeneity. Fortunately, a Python implementation of this functionality already exists as infercnvpy (documentation here).

For an OmicVerse user focused on oncology, analyzing CNVs currently requires exporting the AnnData object, running inferCNV in a separate process, and then importing the results back into the workflow. This procedure disrupts the seamless, all-in-one analytical experience that OmicVerse aims to provide. Integrating this powerful tool would significantly enhance OmicVerse's capabilities for cancer genomics, offering users a complete, end-to-end analysis pipeline—from preprocessing to CNV inference—within a single, unified framework. This would be a highly attractive feature for the rapidly growing Python cancer single-cell community.

Thank you for your consideration!