Package 'msigdbr'

Title: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
Description: Provides the 'Molecular Signatures Database' (MSigDB) gene sets typically used with the 'Gene Set Enrichment Analysis' (GSEA) software (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>, Liberzon et al. 2015 <doi:10.1016/j.cels.2015.12.004>, Castanza et al. 2023 <doi:10.1038/s41592-023-02014-7>) as an R data frame. The package includes the human genes as listed in MSigDB as well as the corresponding symbols and IDs for frequently studied model organisms such as mouse, rat, pig, fly, and yeast.
Authors: Igor Dolgalev [aut, cre] (ORCID: <https://orcid.org/0000-0003-4451-126X>)
Maintainer: Igor Dolgalev <[email protected]>
License: MIT + file LICENSE
Version: 26.1.0
Built: 2026-05-11 09:19:43 UTC
Source: https://github.com/igordot/msigdbr

Help Index

Retrieve the gene sets data frame

Description

Retrieve a data frame of gene sets and their member genes. The original human genes can be converted into their corresponding counterparts in various model organisms, including mouse, rat, pig, zebrafish, fly, and yeast. The output includes gene symbols along with NCBI and Ensembl IDs.

Usage

msigdbr(
  db_species = "HS",
  species = "human",
  collection = NULL,
  subcollection = NULL,
  category = deprecated(),
  subcategory = deprecated()
)

Arguments

db_species

Species abbreviation for the human or mouse databases ("HS" or "MM").
species

Species name for output genes, such as "Homo sapiens" or "Mus musculus". Both scientific and common names are acceptable. Use msigdbr_species() to see the available options.
collection

Collection abbreviation, such as "H" or "C1". Use msigdbr_collections() to see the available options.
subcollection

Sub-collection abbreviation, such as "CGP" or "BP". Use msigdbr_collections() for the available options.
category

[Deprecated] use the collection argument
subcategory

[Deprecated] use the subcollection argument

Details

Historically, the MSigDB resource has been tailored to the analysis of human-specific datasets, with gene sets exclusively aligned to the human genome. Starting with release 2022.1, MSigDB incorporated a database of mouse-native gene sets and was split into human and mouse divisions ("Hs" and "Mm"). Each one is provided in the approved gene symbols of its respective species.

Mouse MSigDB includes gene sets curated from mouse-centric datasets and specified in native mouse gene identifiers, eliminating the need for ortholog mapping.

Value

A tibble (a data frame with class tibble::tbl_df) of gene sets with one gene per row.

References

https://www.gsea-msigdb.org/gsea/msigdb/index.jsp

Examples

# Get all human gene sets
gs <- msigdbr()
head(gs)

# Get all mouse gene sets
gs <- msigdbr(db_species = "MM", species = "Mus musculus")
head(gs)

# Get CGP (chemical and genetic perturbations) gene sets with genes mapped to rat orthologs
gs <- msigdbr(species = "Rattus norvegicus", collection = "C2", subcollection = "CGP")
head(gs)

List the collections available in the msigdbr package

Description

List the collections available in the msigdbr package

Usage

msigdbr_collections(db_species = "HS")

Arguments

db_species

Species abbreviation for the human or mouse databases ("HS" or "MM").

Value

A data frame of the available collections.

Examples

msigdbr_collections()

List the species available in the msigdbr package

Description

List the species available in the msigdbr package

Usage

msigdbr_species()

Value

A data frame of the available species.

Examples

msigdbr_species()