GENAVi: a shiny web application for gene expression normalization, analysis and visualization

BMC Genomics

Table 1 A summary of comparisons between GENAVi and tools with shared functionality

	GENAVi	START	iDEP	DEBrowser	DEGUST	DEIVA	DEApp
Hosting
GUI	Yes	Yes	Yes	Yes	Yes	Yes	Yes
URL hosted	Yes	Yes	Yes	No	Yes	Yes	Yes
Active	Yes	Yes	Yes	Yes	Yes	Yes	Yes
run from R	Yes	Yes	No	Yes	No	No	Yes
Open source	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Docker	Yes	No	Yes	No	No	No	No
User data
Upload	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Prefiltering	Yes	No	Yes	Yes	Yes	No	Yes
Bulk Feature Selection	Yes	No	No	No	No	Yes	No
Normalization
Normalization	Yes	Yes	Yes	Yes	No	No	Yes
Methods Available	4	2	3	3	NA	NA	NA
Visualization
Interactive expression heatmap	Yes	Yes	Yes	Yes	No	No	No
Interactive correlation heatmap	Yes	No	Yes	Yes	No	No	No
Volcano Plot	Yes	Yes	Yes	Yes	Yes	Yes	No
Interactive PCA plotting	Yes	Yes	Yes	Yes	No	No	Yes
2D and 3D PCA plotting	Yes	No	No	No	No	No	No
DEA
DEA with packages	Yes	No	Yes	Yes	Yes	No	Yes
Complex model	Yes	Yes	Yes	Yes	No	No	Yes
lfc shrinkage	Yes	No	No	No	No	No	No
Pathway Analysis
ORA	Yes	No	No	No	No	No	No
GSEA ranking method	Yes	No	Yes	Yes	No	No	No
Enrichment Analysis	Yes	No	Yes	Yes	No	No	No
Reproducible Analysis and Documentation
Session and code report	Yes	No	Yes	No	Yes	No	No
Complete analysis report	Yes	No	Yes	No	No	No	No

ISSN: 1471-2164