Retention of multiplet captures in single-cell RNA sequencing (scRNA-seq) data can hinder identification of discrete or transitional cell populations and associated marker genes. To overcome this challenge, we created DoubletDecon to identify and remove doublets, multiplets of two cells, by using a combination of deconvolution to identify putative doublets and analyses of unique gene expression. Here, we provide the protocol for running DoubletDecon on scRNA-seq data.
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