Tutorial: Easy way to do GO enrichment in R
gravatar for ahmad.moousavi
7 months ago by
Royan Institute, Tehran, Iran
ahmad.moousavi40 wrote:

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:

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

R rna-seq tutorial gene enrichr • 1.1k views
ADD COMMENTlink modified 7 months ago • written 7 months ago by ahmad.moousavi40

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

ADD REPLYlink written 7 months ago by YaGalbi1.3k

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.

ADD REPLYlink modified 6 months ago • written 6 months ago by adnbps0

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

ADD REPLYlink written 4 months ago by bikash251030

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

enriched <- enrichr(genes8000, dbs)
ADD REPLYlink written 4 months ago by ahmad.moousavi40
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