Multiplexed scRNA-seq datasets for reproducing "Multiplets in scRNA-seq data: extent of the problem and efficacy of methods for removal"

This Zenodo record contains all datasets required to reproduce the analyses reported in the manuscript “Multiplets in scRNA-seq data: extent of the problem and efficacy of methods for removal” accepted in PLOS ONE (2025).Contains three previously published datasets (cline-ch, mkidney-ch, and pbmc-ch) from 10.5281/zenodo.4062231, where they were used to benchmark multiplet identification tools. The multiplet labels from these datasets have been converted to 0/1 format (1 for multiplet) to unify metadata and streamline processing. Also included is a modified 10x Genomics dataset "Demultiplexing 5’ Immune Profiling Libraries Pooled with Hashtags" (CC BY 4.0) available at 5-hashing-example, where all droplets (including cell-hashing multiplets) associated with donors 3 and 4 with ALL were excluded from the analysis to avoid unexpected interactions stemming from abnormal gene expression in cancer cells. This dataset was processed with 10X Genomics' Cell Ranger as detailed in the aforementioned manuscript to get a gene by droplet expression matrix and multiplet labels from demultiplexing.