TABLE 1.

Time comparison of functionalities for different test data.

Type of analysis		Time (s)
		Test 1*	Test 2#	Test 3∧
Pre-processing	TPM/RPKM/FPKM and RLE plot	−	−	$0.6\mathrm{s}$
	Upper quartile normalization and RLE plot	−	$0.5\mathrm{s}$	$0.6\mathrm{s}$
	RUV normalization and RLE plot	$1.7\mathrm{s}$	−	−
Scatter plot		$0.01\mathrm{s}$	$0.01\mathrm{s}$	$0.01\mathrm{s}$
Distribution fitting (for all 6 distributions)		$4.3\mathrm{s}$	$3.1\mathrm{s}$	$2.5\mathrm{s}$
Correlation matrix		0.01	$0.01\mathrm{s}$	$0.01\mathrm{s}$
PCA calculation and plotting		0.01	0.01	0.01
DE analysis	edgeR	7.89	$1.52\mathrm{s}$	$5.23\mathrm{s}$
	DESeq2	$15.4\mathrm{s}$	$3.1\mathrm{s}$	$11.3\mathrm{s}$
	NOISeq	$29.6\mathrm{s}$	$22.87\mathrm{s}$	$31.0\mathrm{s}$
Heat map and hierarchical clustering	DE (using edgeR result) (5 clusters)	$0.36\mathrm{s}$	$1.7\mathrm{s}$	$0.25\mathrm{s}$
	Independent (5 clusters)	$30.4\mathrm{s}$	$7.7\mathrm{s}$	$4.6\mathrm{s}$
Noise		$3.2\mathrm{s}$	$1.3\mathrm{s}$	$3.9\mathrm{s}$
Shannon entropy		$0.03\mathrm{s}$	$0.02\mathrm{s}$	$0.08\mathrm{s}$
GO analysis (using edgeR result)	clusterProfiler	$20.2\mathrm{s}$	$10.3\mathrm{s}$	$9.1\mathrm{s}$
	GOstats	$26.6\mathrm{s}$	$10.2\mathrm{s}$	$12.3\mathrm{s}$
	EnrichR	−	−	−

^*Risso et al., 2014: GEO accession number: GSE53334. #Bendjilali et al., 2017: GEO accession number: GSE85595. ^∧Cromie et al., 2017: GEO accession number: GSE85843.