The msigdbr R package provides Molecular Signatures Database (MSigDB) gene sets typically used with the Gene Set Enrichment Analysis (GSEA) software:
- in an R-friendly tidy/long format with one gene per row
- for multiple frequently studied model organisms, such as mouse, rat, pig, zebrafish, fly, and yeast, in addition to the original human genes
- as both gene symbols and NCBI/Entrez Gene IDs for better compatibility with pathway enrichment tools
- that can be installed and loaded as a package without requiring additional external files
The package can be installed from CRAN.
install.packages("msigdbr")
The package data can be accessed using the msigdbr() function, which returns a data frame of gene sets and their member genes. For example, you can retrieve mouse genes from the C2 (curated) CGP (chemical and genetic perturbations) gene sets.
genesets = msigdbr(species = "Mus musculus", category = "C2", subcategory = "CGP")
Check the documentation website for more information.