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Table 1 Comparison of applications for analyzing RNA-Seq

From: iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data

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