| 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>) in a standard R data frame with key-value pairs. 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] |
| Maintainer: | Igor Dolgalev <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 7.5.1.9001 |
| Built: | 2024-08-13 03:17:26 UTC |
| Source: | https://github.com/igordot/msigdbr |
Retrieve a data frame of gene sets and their member genes.
The available species and collections can be checked with msigdbr_species() and msigdbr_collections().
msigdbr(species = "Homo sapiens", category = NULL, subcategory = NULL)msigdbr(species = "Homo sapiens", category = NULL, subcategory = NULL)
species |
Species name, such as Homo sapiens or Mus musculus. |
category |
MSigDB collection abbreviation, such as H or C1. |
subcategory |
MSigDB sub-collection abbreviation, such as CGP or BP. |
A data frame of gene sets with one gene per row.
https://www.gsea-msigdb.org/gsea/msigdb/collections.jsp
# get all human gene sets msigdbr(species = "Homo sapiens") # get mouse C2 (curated) CGP (chemical and genetic perturbations) gene sets msigdbr(species = "Mus musculus", category = "C2", subcategory = "CGP")# get all human gene sets msigdbr(species = "Homo sapiens") # get mouse C2 (curated) CGP (chemical and genetic perturbations) gene sets msigdbr(species = "Mus musculus", category = "C2", subcategory = "CGP")
List the collections available in the msigdbr package
msigdbr_collections()msigdbr_collections()
A data frame of the available collections.
msigdbr_collections()msigdbr_collections()
This function is being deprecated and replaced by msigdbr_species().
msigdbr_show_species()msigdbr_show_species()
A vector of possible species.
List the species available in the msigdbr package
msigdbr_species()msigdbr_species()
A data frame of the available species.
msigdbr_species()msigdbr_species()