msigdbr: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format

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Overview

The msigdbr R package provides Molecular Signatures Database (MSigDB) gene sets typically used with the Gene Set Enrichment Analysis (GSEA) software:

Installation

The package can be installed from CRAN.

install.packages("msigdbr")

Recent releases are not available on CRAN and can be installed from GitHub (specific version can be specified):

remotes::install_github("igordot/msigdbr", ref = "v2022.1.1")

Usage

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.

library(msigdbr)
genesets <- msigdbr(species = "mouse", category = "C2", subcategory = "CGP")

Check the documentation website for more information.