Identification and Removal of Doublets with DoubletDecon

Abstract

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. For complete details on the use of this protocol, please see DePasquale et al. (2019) (https://doi.org/10.1016/j.celrep.2019.09.082). GRAPHICAL ABSTRACT O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY