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.
devtools::install_github("mw201608/msigdb")
To install a previous release of MSigDB v6.1:
devtools::install_github("mw201608/msigdb@cc6785981f12de23650911d64a646c807bbe04be")
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:
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