The msigdbr R package provides Molecular Signatures Database (MSigDB) gene sets typically used with the Gene Set Enrichment Analysis (GSEA) software:
Details and examples are described in the vignette.
The package can be installed from CRAN.
Load package.
Check the available species.
msigdbr_show_species()
#> [1] "Bos taurus" "Caenorhabditis elegans" "Canis lupus familiaris"
#> [4] "Danio rerio" "Drosophila melanogaster" "Gallus gallus"
#> [7] "Homo sapiens" "Mus musculus" "Rattus norvegicus"
#> [10] "Saccharomyces cerevisiae" "Sus scrofa"Retrieve all human gene sets.
m_df = msigdbr(species = "Homo sapiens")
head(m_df)
#> # A tibble: 6 x 9
#> gs_name gs_id gs_cat gs_subcat human_gene_symb… species_name entrez_gene gene_symbol
#> <chr> <chr> <chr> <chr> <chr> <chr> <int> <chr>
#> 1 AAACCAC_M… M126… C3 MIR ABCC4 Homo sapiens 10257 ABCC4
#> 2 AAACCAC_M… M126… C3 MIR ACTN4 Homo sapiens 81 ACTN4
#> 3 AAACCAC_M… M126… C3 MIR ACVR1 Homo sapiens 90 ACVR1
#> 4 AAACCAC_M… M126… C3 MIR ADAM9 Homo sapiens 8754 ADAM9
#> 5 AAACCAC_M… M126… C3 MIR ADAMTS5 Homo sapiens 11096 ADAMTS5
#> 6 AAACCAC_M… M126… C3 MIR AGER Homo sapiens 177 AGER
#> # ... with 1 more variable: sources <chr>Retrieve mouse hallmark collection gene sets.
m_df = msigdbr(species = "Mus musculus", category = "H")
head(m_df)
#> # A tibble: 6 x 9
#> gs_name gs_id gs_cat gs_subcat human_gene_symb… species_name entrez_gene gene_symbol
#> <chr> <chr> <chr> <chr> <chr> <chr> <int> <chr>
#> 1 HALLMARK_… M5905 H "" ABCA1 Mus musculus 11303 Abca1
#> 2 HALLMARK_… M5905 H "" ABCB8 Mus musculus 74610 Abcb8
#> 3 HALLMARK_… M5905 H "" ACAA2 Mus musculus 52538 Acaa2
#> 4 HALLMARK_… M5905 H "" ACADL Mus musculus 11363 Acadl
#> 5 HALLMARK_… M5905 H "" ACADM Mus musculus 11364 Acadm
#> 6 HALLMARK_… M5905 H "" ACADS Mus musculus 11409 Acads
#> # ... with 1 more variable: sources <chr>