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Understanding how genome changes shape gene expression in individual cells is essential to understand complex genetic diseases such as cancers. Latest high-throughput single-cell RNA (scRNA-) and DNA-sequencing (scDNA-seq) technologies enabled cell-resolved investigation of pathological tissue clones. However, it is still technically challenging to simultaneously measure the genome and transcriptome content of a single cell. In this work, we developed CCNMF--a new computational tool utilizingdoi:10.1101/2020.02.04.934455 fatcat:taghxbtpavcsvdiyyjrtcb2c3a