msigdb

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13

An ExperimentHub Package for the Molecular Signatures Database (MSigDB)

Bioconductor version: Development (3.24)

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] ORCID: 0000-0002-6398-9157 , Gordon K. Smyth [aut] ORCID: 0000-0001-9221-2892 , Alexandra Garnham [aut] ORCID: 0000-0002-8312-8450

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

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

Dharmesh D. Bhuva, Gordon K. Smyth, Alexandra Garnham. msigdb: An ExperimentHub Package for the Molecular Signatures Database (MSigDB). doi:10.18129/B9.bioc.msigdb, R package version 1.21.0, https://bioconductor.org/packages/msigdb.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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")

msigdb	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, ExperimentHub, Homo_sapiens_Data, Mus_musculus_Data
Version	1.21.0
In Bioconductor since	BioC 3.13 (R-4.1) (5.5 years)
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

Suggests	singscore, vissE, knitr, prettydoc, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocFileCache, GO.db, stringr, limma
Linking To
Enhances
Depends On Me
Imports Me	mastR, postNet, singIST, vissE
Suggests Me	escape
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	msigdb_1.21.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-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/
Package Downloads Report	Download Stats