1 Overview

clonealign assigns cells measured using single-cell RNA-seq to their clones of origin using copy number data. This is especially useful when clones are inferred from shallow single-cell DNA-seq, in which case the copy number state of each clone is known, but the precise SNV structure is unknown.

To assign cells to clones, clonealign makes the assumption that

$\text{gene expression} \propto \text{number of gene copies}$

This is demonstrated in the figure below.