Version Compatibility

Reference examples tested with: inferCNV 1.18+, copyKAT 1.1+, numbat 1.4+, SCEVAN 1.0+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Copy-Number Inference from Single-Cell RNA-seq

"Which cells are tumor, and what CNVs and subclones do they carry?" -> Estimate large-scale copy-number from smoothed expression across genomic windows, compare against a normal reference, and cluster cells into malignant vs normal and into subclones.

• R (reference-based, expression-only): inferCNV - smooth expression along chromosomes against a defined normal reference, optional HMM for discrete CNV states
• R (reference-free, expression-only): copyKAT, SCEVAN - estimate the diploid baseline internally and segment, then classify aneuploid vs diploid
• R (haplotype-aware, allele + expression): Numbat - add phased B-allele frequency for the best subclone and copy-neutral-LOH resolution

Governing principle