Skip to content

willgryan/enrichR

 
 

Repository files navigation

An R interface to the Enrichr database

Wajid Jawaid 2021-02-02

CRAN_Status_Badge Project Status: Active - The project has reached a stable, usable state and is being actively developed. CRAN mirror downloads

Installation

enrichR can be installed from Github or from CRAN.

Github

library(devtools)
install_github("wjawaid/enrichR")

CRAN

The package can be downloaded from CRAN using:

install.packages("enrichR")

Usage example

enrichR provides an interface to the Enrichr database [@kuleshov_enrichr:_2016] hosted at https://maayanlab.cloud/Enrichr/.

By default human genes are selected otherwise select your organism of choice. (This functionality was contributed by Alexander Blume)

library(enrichR)
listEnrichrSites()
#> Enrichr ... Connection is Live!
#> FlyEnrichr ... Connection is available!
#> WormEnrichr ... Connection is available!
#> YeastEnrichr ... Connection is available!
#> FishEnrichr ... Connection is available!
setEnrichrSite("Enrichr") # Human genes
#> Connection changed to https://maayanlab.cloud/Enrichr/
#> Connection is Live!

Then find the list of all available databases from Enrichr.

dbs <- listEnrichrDbs()

head(dbs)
geneCoverage genesPerTerm libraryName numTerms
13362 275 Genome_Browser_PWMs 615
27884 1284 TRANSFAC_and_JASPAR_PWMs 326
6002 77 Transcription_Factor_PPIs 290
47172 1370 ChEA_2013 353
47107 509 Drug_Perturbations_from_GEO_2014 701
21493 3713 ENCODE_TF_ChIP-seq_2014 498

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")
enriched <- enrichr(c("Runx1", "Gfi1", "Gfi1b", "Spi1", "Gata1", "Kdr"), dbs)
#> Uploading data to Enrichr... Done.
#>   Querying GO_Molecular_Function_2015... Done.
#>   Querying GO_Cellular_Component_2015... Done.
#>   Querying GO_Biological_Process_2015... Done.
#> Parsing results... Done.

Now view the results table.

enriched[["GO_Biological_Process_2015"]]

You can give many genes.

data(genes790)
length(genes790)
head(enrichr(genes790, c('LINCS_L1000_Chem_Pert_up'))[[1]])
Term Overlap P.value Adjusted.P.value Old.P.value Old.Adjusted.P.value Odds.Ratio Combined.Score Genes
embryonic hemopoiesis (GO_0035162) 3/24 0.0e+00 0.0000083 0 0 951.0952 16465.833 KDR;GATA1;RUNX1
regulation of myeloid cell differentiation (GO_0045637) 4/156 1.0e-07 0.0000083 0 0 261.0789 4374.968 GFI1B;SPI1;GATA1;RUNX1
regulation of erythrocyte differentiation (GO_0045646) 3/36 1.0e-07 0.0000112 0 0 604.8788 9710.235 GFI1B;SPI1;GATA1
positive regulation of myeloid cell differentiation (GO_0045639) 3/74 1.0e-06 0.0000762 0 0 280.6056 3886.803 GFI1B;GATA1;RUNX1
hemopoiesis (GO_0030097) 3/95 2.1e-06 0.0001299 0 0 216.3261 2832.846 KDR;GATA1;RUNX1
hematopoietic progenitor cell differentiation (GO_0002244) 3/106 2.9e-06 0.0001507 0 0 193.1165 2465.031 SPI1;GATA1;RUNX1

Plot Enrichr GO-BP output. (Plotting function contributed by I-Hsuan Lin)

plotEnrich(enriched[[3]], showTerms = 20, numChar = 40, y = "Count", orderBy = "P.value")

References

Kuleshov, Maxim V., Matthew R. Jones, Andrew D. Rouillard, Nicolas F. Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, et al. 2016. “Enrichr: A Comprehensive Gene Set Enrichment Analysis Web Server 2016 Update.” Nucleic Acids Res 44 (Web Server issue): W90–W97. https://doi.org/10.1093/nar/gkw377.

About

An R interface to enrichR

Resources

Stars

Watchers

Forks

Packages

No packages published

Languages

  • R 91.6%
  • TeX 8.4%