Retrieve Organism-specific MSigDB Gene Sets

get_mgsigdb_gsets(species = "Homo sapiens", collection, subcollection = NULL)



species name, such as Homo sapiens, Mus musculus, etc. See msigdbr_show_species for all the species available in the msigdbr package


collection. i.e., H, C1, C2, C3, C4, C5, C6, C7.


sub-collection, such as CGP, BP, etc. (default = NULL, i.e. list all gene sets in collection)


Retrieves the MSigDB gene sets and returns a list containing 2 elements:

  • gene_setsA list containing the genes involved in each of the selected MSigDB gene sets

  • descriptionsA named vector containing the descriptions for each selected MSigDB gene set


this function utilizes the function msigdbr from the msigdbr package to retrieve the 'Molecular Signatures Database' (MSigDB) gene sets (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>, Liberzon et al. 2015 <doi:10.1016/j.cels.2015.12.004>). Available collections are: H: hallmark gene sets, C1: positional gene sets, C2: curated gene sets, C3: motif gene sets, C4: computational gene sets, C5: GO gene sets, C6: oncogenic signatures and C7: immunologic signatures