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

Overview

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 gene symbols as well as NCBI Entrez and Ensembl IDs
• that can be installed and loaded as a package without requiring additional external files

Installation

The package can be installed from CRAN.

install.packages("msigdbr")

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.

genesets = msigdbr(species = "Mus musculus", category = "C2", subcategory = "CGP")

Check the documentation website for more information.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.