Table 3 Benchmark of Genekitr and existing enrichment analysis webservers
From: Empowering biologists to decode omics data: the Genekitr R package and web server
Tool | Method | Gene set libraries | No. of species | No. of plotting types | Customizable plotting | Image type | GO simplification | Availability |
|---|---|---|---|---|---|---|---|---|
WebGestalt [9] | ORA, GSEA, PTa | GO, KEGG, + 20 more | 12 | 5 | No | PNG, SVG | No | - webserver - R - API |
KOBAS [52] | ORA, CGPSb | GO, KEGG, + 3 more | - GO: 71—BioCyc: 18 - KEGG: 5944—Reactome: 14 - PANTHER: 41 | 3 | No | PNG | No | - webserver - Python program |
g:Profiler [6] | ORA | GO, KEGG, + 7 more | - GO: 821—MIRNA: 16 - KEGG: 255—WikiPathways: 13 - TF: 9 - HP: 414 - CORUM: 3 | 2 | No | PNG | No | - webserver - R - API |
DAVID [7] | ORA | GO, KEGG, + 77 more |  > 65,000 | – | – | – | No | - webserver - API |
Gorilla [53] | ORA | GO | 8 | 1 | – | PNG | No | webserver |
ToppGene [56] | ORA | GO, KEGG, + 135 more | 2 | 1 | No | HTML | No | - webserver - API |
bioDBnet [49] | ORA | GO, KEGG, + 4 more | 6 | – | – | – | No | - webserver - API |
agriGO [57] | ORA, GSEA | GO | 404 | 2 | Yes | PNG, JPEG, GIF, SVG, PDF | No | webserver |
Revigo [54] | ORA | GO | 25 | – | – | – | No | webserver |
PANTHER [43] | ORA, GSEA | GO, KEGG | 143 | 5 | No | SVG | No | webserver |
Enrichr [10] | ORA | GO, KEGG, + 274 more | 6 | 4 | No | SVG, PNG, JPG | No | webserver |
FunSet [55] | ORA | GO | 11 | 1 | No | SVG | No | - webserver - API |
ShinyGO [12] | ORA | GO | 315 | 6 | Yes | PDF, PNG, SVG | No | webserver |
Genekitr | ORA, GSEA | GO, KEGG, + 313 more | - GO: 143—MSigDB: 20 - KEGG: 8213—Enrichr: 5 - Reactome: 11—WikiPathways: 16 - MeSH: 71—Disease specificc: 1 | - ORA: 13 - GSEA: 5 | Yes | EPS, EMF, PPT, PNG, TIFF, JPEG | Yes | - webserver - R |