Table 1 Comparison of applications for analyzing RNA-Seq

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