msigdb

DOI: 10.18129/B9.bioc.msigdb    

This is the development version of msigdb; for the stable release version, see msigdb.

An ExperimentHub Package for the Molecular Signatures Database (MSigDB)

Bioconductor version: Development (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>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.0
License CC BY 4.0
Depends R (>= 4.1)
Imports ExperimentHub, utils, GSEABase, org.Mm.eg.db, org.Hs.eg.db, AnnotationDbi, methods, stats
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_1.1.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: