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msigdb's Introduction

MSigDB Gene Set Collections

This R package contains the MSigDB gene set collections (version 7.1 downloaded on June 22, 2020). 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.BP','C5.CC', 'C5.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

msigdb's People

Contributors

mw201608 avatar mschubert avatar

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