Are there methods for identifying multiplets?

Question: Are there methods for identifying multiplets or doublets in single-cell gene expression analysis?

Answer: At present, there is no explicit support for multiplet identification in the Cell Ranger gene expression analysis pipeline other than for the analysis of "barnyard" or mixed-species datasets mapped to a multiple-species reference.

Below are some third-party tools for detecting doublets/multiplets in single-cell gene expression datasets:

• Scrublet:
  • https://www.biorxiv.org/content/early/2018/07/09/357368
  • https://github.com/AllonKleinLab/scrublet 
• DoubletDecon:
  • https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31286-0 
  • https://github.com/EDePasquale/DoubletDecon 
• DoubletFinder:
  • https://www.cell.com/cell-systems/fulltext/S2405-4712(19)30073-0  
  • https://github.com/chris-mcginnis-ucsf/DoubletFinder
• Solo:
  • https://www.cell.com/cell-systems/fulltext/S2405-4712(20)30195-2
  • https://github.com/calico/solo/blob/master/README.md 

Please contact the respective developers of each tool for more information.

Disclaimer: This article and code-snippet are provided for instructional purposes only. 10x Genomics does not support or guarantee the code.