README.md

In mw201608/msigdb: MSigDB Gene Set Collections

MSigDB Gene Set Collections

This R package contains the MSigDB gene set collections (version 7.4 downloaded on August 9, 2021). To avoid a conflict with Bioconductor/msigdb, this package has been renamed to msigdbi. The official MSigDB website is https://www.gsea-msigdb.org/gsea/index.jsp.

Installation

devtools::install_github("mw201608/msigdb")

To install a previous release of MSigDB v6.1:

devtools::install_github("mw201608/msigdb@cc6785981f12de23650911d64a646c807bbe04be")

Usage

See help documentation ?msigdb.genesets for how to loading the gene sets. For example, to load human gene ontology (GO) gene sets:

Result = msigdb.genesets(sets = c('c5.go.bp','c5.go.cc', 'c5.go.mf'), type = 'symbols', species = 'human')

To see all available gene sets, see variable

msigdb.collections

Examples of performing functional enrichment analysis with the MSigDB gene sets can be found in two packages:

1. GOtest, available at https://github.com/mw201608/GOtest

2. GOplot, available at https://github.com/ericaenjoy3/GOplot (to be updated to work with renamed msigdbi)

mw201608/msigdb documentation built on Aug. 13, 2021, 10:42 p.m.