DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

. Author manuscript; available in PMC: 2019 Nov 13.

Published in final edited form as: Cell Syst. 2019 Apr 3;8(4):329–337.e4. doi: 10.1016/j.cels.2019.03.003

KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited Data
soRNA-seq-UMI counts of PBMCs demultiplexed using Demuxlet	Kang et al., 2018	GEO: GSE96583
scRNA-seq-UMI counts of PBMCs demultiplexed using Cell Hashing	Stoeckius et al., 2018	GEO:GSE108313
scRNA-seq-UMI counts of mouse kidney cells	Park et al., 2018	GEO: GSE107585
scRNA-seq-UMI counts of mouse pancreas cells	Byrnes et al., 2018	GEO:GSE101099
Software and Algorithms
Seurat	Satija et al., 2015 Butler et al., 2018	https://github.com/satijalab/seurat
Splatter	Zappia et al., 2017	https://github.com/Oshlack/splatter
ROCR	Sing et al., 2005	https://github.com/ipa-tys/ROCR
pROC	Robin et al., 2011	https://github.com/xrobin/pROC
Caret	Kuhn, 2008	https://cran.r-project.org/web/packages/caret/caret.pdf
Modes	Deevi, 2016	https://cran.r-project.org/web/packages/modes/modes.pdf
Fields	Nychka et al., 2017	https://cran.r-project.org/web/packages/fields/fields.pdf
DoubletFinder	This paper	https://github.com/chris-mcginnis-ucsf/DoubletFinder