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Bioconductor - msigdb (development version)

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 (3.22)

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")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("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")
Details biocViews ExperimentData, ExperimentHub, Homo_sapiens_Data, Mus_musculus_Data Version 1.17.0 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 Enhances Depends On Me Imports Me mastR, vissE Suggests Me epiregulon.extra, escape Links To Me Build Report Build Report Package Archives

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


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