Table 3
Subpopulation identification methods for scRNA-seq data.
Methods
URL
References
SC3
http://bioconductor.org/packages/SC3
Kiselev et al., 2017
ZIFA
https://github.com/epierson9/ZIFA
Pierson and Yau, 2015
Destiny
https://github.com/theislab/destiny
Angerer et al., 2016
SNN-Cliq
http://bioinfo.uncc.edu/SNNCliq/
Xu and Su, 2015
RaceID
https://github.com/dgrun/RaceID
Grun et al., 2015
SCUBA
https://github.com/gcyuan/SCUBA
Marco et al., 2014
BackSPIN
https://github.com/linnarsson-lab/BackSPIN
Zeisel et al., 2015
PAGODA
http://hms-dbmi.github.io/scde/
Fan et al., 2016
CIDR
https://github.com/VCCRI/CIDR
Lin et al., 2017
pcaReduce
https://github.com/JustinaZ/pcaReduce
Zurauskiene and Yau, 2016
Seurat
https://github.com/satijalab/seurat
Satija et al., 2015
TSCAN
https://github.com/zji90/TSCAN
Ji and Ji, 2016