msigdb

DOI: 10.18129/B9.bioc.msigdb    

An ExperimentHub Package for the Molecular Signatures Database (MSigDB)

Bioconductor version: Release (3.14)

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>

Installation

To install this package, start R (version "4.1") 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")

 

HTML	R Script	msigdb
PDF		Reference Manual
Text		NEWS

Details

biocViews	ExperimentData, ExperimentHub, Homo_sapiens_Data, Mus_musculus_Data
Version	1.2.0
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
LinkingTo
Suggests	singscore, vissE, knitr, prettydoc, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocFileCache, GO.db, stringr, limma
SystemRequirements
Enhances
URL	https://davislaboratory.github.io/msigdb
BugReports	https://github.com/DavisLaboratory/msigdb/issues
Depends On Me
Imports Me	vissE
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	msigdb_1.2.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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/
Package Downloads Report	Download Stats