  The existence of doublets is a key confounder in single-cell RNA sequencing
(scRNA-seq) data analysis. Computational methods have been developed for
detecting doublets from scRNA-seq data. We developed an R package
DoubletCollection to integrate the installation and execution of eight
doublet-detection methods. DoubletCollection also provides a unified interface
to perform and visualize downstream analysis after doublet detection. Here, we
present a protocol of using DoubletCollection to benchmark doublet-detection
methods. This protocol can automatically accommodate new doublet-detection
methods in the fast-growing scRNA-seq field.
