Tutorial:Easy way to do GO enrichment in R

Question

[ahmad mousavi]

Hi friends

After all I found a way to do GO enrichment in a programming and very easy way. You should install enrichR package and then use following code:

library(enrichR)
dbs <- listEnrichrDbs()
dbs <- c("GO_Molecular_Function_2015", "GO_Cellular_Component_2015", "GO_Biological_Process_2015" , "ChEA_2016" ,"KEGG_2016")
enriched <- enrichr(c("Runx1", "Gfi1", "Gfi1b", "Spi1", "Gata1", "Kdr"), dbs)
printEnrich(enriched, "output.txt" , sep = "\t", columns = c(1:9))

bp <- enriched[["GO_Biological_Process_2015"]]

Thanks guys who developed this package!

Cheers :D

[BioinfGuru]

Enrichr R is very useful because of multiple enrichment analyses in one place....however, when you go through the paper you will notice that part of their algorithm for producing the combined score is "intuition".

Because I don;t like black boxes...I stick to g:Profiler

[adnbps]

enrichr was published in a good journal (NAR) and is not exactly a black box. While they provide a correction to the Fisher exact test, you don't have to use it. They also give you the uncorrected p-values. Of course, you should use whatever tool you prefer, but I don't want to give other people the false impression that enrichr is statistically unprincipled.

[bikash2510]

How to add or input nearly 8000 genes for annotation in enrichR.

[ahmad mousavi]

just paste your gene in enrichR website; in R you could input your genes as a vector in below code :

enriched <- enrichr(genes8000, dbs)

Answer 1

[Kevin Blighe]

topGo is one program - see my answers, here:

• GO analysis using topGO
• plotting a dotplot with topGO output

Kevin