CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data

Table 1 Runtime comparison between CIDR and four other algorithms

Data set	Size	CIDR	CIDR (L)	prcomp	t-SNE	RaceID	ZIFA
Pancreatic islet	60	5.2 s	5.3 s	2.9 s	8.5 s	48.6 s	40.1 min
Simulation	150	1.9 s	2.3 s	2.9 s	14.2 s	20.7 s	32.1 min
Human brain	420	6.6 s	8.9 s	13.7 s	1.4 min	1.5 min	1.1 h
Mouse brain	1800	57.9 s	1.1 min	3.2 min	23.1 min	2.5 h^a	1.8 h

CIDR is the default CIDR algorithm implementation with step function simplification, while CIDR (L) is the implementation with the non-simplified logistic function. The algorithms were run on a standard laptop: 2.8 GHz Intel Core i5 (I5-4308U), 8GB DDR3 RAM)
^aRaceID failed to converge for the mouse brain data set

ISSN: 1474-760X