Easy loading of gene set databases

Here are some shortcuts to load common databases:

library(zenith)

## MSigDB as ENSEMBL genes
# all genesets in MSigDB
gs.msigdb = get_MSigDB()

# only Hallmark gene sets
gs = get_MSigDB('H')

# only C1
gs = get_MSigDB('C1')

# C1 and C2
gs = get_MSigDB(c('C1', 'C2'))

# C1 as gene SYMBOL
gs = get_MSigDB('C1', to="SYMBOL")

# C1 as gene ENTREZ
gs = get_MSigDB('C1', to="ENTREZ")

## Gene Ontology
gs.go = get_GeneOntology()

# load Biological Process and gene SYMBOL
gs.go = get_GeneOntology("BP", to="SYMBOL")

Other databases

EnrichmentBrowser provides additional databases (i.e. KEGG, Enrichr), alternate gene identifiers (i.e. ENSEMBL, ENTREZ) or species (i.e. hsa, mmu)

library(EnrichmentBrowser)

# KEGG
gs.kegg = getGenesets(org = "hsa", 
                      db = "kegg", 
                      gene.id.type = "ENSEMBL", 
                      return.type = "GeneSetCollection")

## ENRICHR resource
# provides many additional gene set databases
df = showAvailableCollections( org = "hsa", db = "enrichr")

head(df)

# Allen_Brain_Atlas_10x_scRNA_2021
gs.allen = getGenesets( org = "hsa", 
                        db = "enrichr", 
                        lib = "Allen_Brain_Atlas_10x_scRNA_2021",
                        gene.id.type = "ENSEMBL", 
                        return.type = "GeneSetCollection")

Custom gene sets

# Load gene sets from GMT file
gmt.file <- system.file("extdata/hsa_kegg_gs.gmt",
                       package = "EnrichmentBrowser")
gs <- getGenesets(gmt.file)     

Session Info

## R version 4.5.1 (2025-06-13)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] knitr_1.50
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.37     R6_2.6.1          fastmap_1.2.0     xfun_0.53        
##  [5] maketools_1.3.2   cachem_1.1.0      htmltools_0.5.8.1 rmarkdown_2.30   
##  [9] buildtools_1.0.0  lifecycle_1.0.4   cli_3.6.5         sass_0.4.10      
## [13] jquerylib_0.1.4   compiler_4.5.1    sys_3.4.3         tools_4.5.1      
## [17] evaluate_1.0.5    bslib_0.9.0       yaml_2.3.10       jsonlite_2.0.0   
## [21] rlang_1.1.6