enrichR can be installed from Github or soon from CRAN.
library(devtools)
install_github("wjawaid/enrichR")
The package can be downloaded from CRAN using:
install.packages("enrichR")
enrichR provides an interface to the Enrichr database [@kuleshov_enrichr:_2016] hosted at http://amp.pharm.mssm.edu/Enrichr.
First find the list of all available databases from Enrichr.
library(enrichR)
dbs <- listEnrichrDbs()
## EnrichR website not responding
if (is.null(dbs)) websiteLive <- FALSE
if (websiteLive) head(dbs)
## Warning in kable_markdown(x = structure(character(0), .Dim = c(0L,
## 0L), .Dimnames = list(: The table should have a header (column names)
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View and select your favourite databases. Then query enrichr, in this case I have used genes associated with embryonic haematopoiesis.
dbs <- c("GO_Molecular_Function_2015", "GO_Cellular_Component_2015", "GO_Biological_Process_2015")
if (websiteLive) enriched <- enrichr(c("Runx1", "Gfi1", "Gfi1b", "Spi1", "Gata1", "Kdr"), dbs)
## EnrichR website not responding
Now view the results table.
if (websiteLive) enriched[["GO_Biological_Process_2015"]]
## Warning in kable_markdown(x = structure(character(0), .Dim = c(0L,
## 0L), .Dimnames = list(: The table should have a header (column names)
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