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cnv-inference

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Infer large-scale copy-number alterations from tumor single-cell or single-nucleus RNA-seq to separate malignant from normal cells and call subclones, using inferCNV, copyKAT, Numbat, and SCEVAN. Use when separating malignant from normal cells in a tumor scRNA-seq dataset, inferring chromosome-arm CNVs or aneuploidy from expression, calling tumor subclones from single cells, choosing a CNV-inference method (reference-based vs reference-free, expression-only vs allele-aware), or deciding which cells are tumor before downstream analysis.

When to use

• separating malignant from normal cells in tumor scRNA-seq
• inferring chromosome-arm CNVs or aneuploidy from expression
• calling tumor subclones from single cells
• choosing a CNV-inference method
• deciding which cells are tumor before downstream analysis

When not to use

• focal gene or exon resolution
• DNA-based copy-number analysis
• integrating or batch-correcting cells across patients before inference
• detecting balanced whole-genome doubling
• detecting CNV-quiet tumors without orthogonal evidence

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