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msigdb

An ExperimentHub Package for the Molecular Signatures Database (MSigDB)


Bioconductor version: Release (3.18)

This package provides the Molecular Signatures Database (MSigDB) in a R accessible objects. Signatures are stored in GeneSet class objects form the GSEABase package and the entire database is stored in a GeneSetCollection object. These data are then hosted on the ExperimentHub. Data used in this package was obtained from the MSigDB of the Broad Institute. Metadata for each gene set is stored along with the gene set in the GeneSet class object.

Author: Dharmesh D. Bhuva [aut, cre] , Gordon K. Smyth [aut] , Alexandra Garnham [aut]

Maintainer: Dharmesh D. Bhuva <bhuva.d at wehi.edu.au>

Citation (from within R, enter citation("msigdb")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("msigdb")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("msigdb")
msigdb HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ExperimentData, ExperimentHub, Homo_sapiens_Data, Mus_musculus_Data
Version 1.10.0
License CC BY 4.0
Depends R (>= 4.1)
Imports ExperimentHub, utils, GSEABase, org.Mm.eg.db, org.Hs.eg.db, AnnotationDbi, methods, stats, AnnotationHub
System Requirements
URL https://davislaboratory.github.io/msigdb
Bug Reports https://github.com/DavisLaboratory/msigdb/issues
See More
Suggests singscore, vissE, knitr, prettydoc, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocFileCache, GO.db, stringr, limma
Linking To
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Depends On Me
Imports Me mastR, vissE
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package msigdb_1.10.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/msigdb
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/msigdb
Package Short Url https://bioconductor.org/packages/msigdb/
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