Skip to main content

Table 1 Runtime comparison between CIDR and four other algorithms

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

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 ha 1.8 h
  1. 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)
  2. aRaceID failed to converge for the mouse brain data set