Table 1.

Comparison of applications for analyzing RNA-Seq

	START App	Degust	ShinyNGS	DEIVA	VisRseq	ASAP	EXPath Tool	IRIS	iDEP
Heatmap	O		O		O	O		O	O
PCA/MDS	O	O	O		O	O		O	O
Clustering of genes			O	O	O			O	O
Volcano/MA Plot	O	O	O	O	O			O	O
Single gene plot	O	O			O				O
Diff. gene expression	O	O	O			O	O	O	O
Co-expression							O		O
Stand-alone R code		O	O			O			O
Pathway analysis		KEGG	KEGG			human& mouse	O		O
Gene ID conversion									O
API to KEGG, STRING-db									O
Complex models								O	O

Note: “O” indicates the functionality is included in a tool.