Table 2. Comparison of a bioinformatics platform for downstream analysis.

	iDEP	IRIS-EDA	START App	ShinyNGS	DEBrowser	OMnalysis
Input data	Count data, meta-data	Count data	Count or expression data	Count or expression data	Count data	Expression data (list of DEGs or Proteins)
PCA	√	√	√	√	√	√
Volcano/Scatter plot	√	√	√	X	√	√
GO analysis	√	X	X	√	√	√
Pathway analysis	√	X	X	X	√	√
Gene ID conversion	√	X	X	X	X	√
Pathway databases	KEGG, STRING API	X	X	KEGG	KEGG	KEGG, Reactome, NCI, Panther, biocarta, PharmGKB, STRING
Literature retrieval	X	X	X	X	X	√
Application type	Online	Online	Online	Require R for online	Require R for online	Online
Stand-alone R code	√	√	√	√	√	√
Pathway visualization and STRING network	√	X	X	X	√	KEGG, Reactome, PPI network

Notes.

X and √ indicates non-available and available function in the tool, respectively.