msigdb
This is thereleased version of msigdb; for the devel version, seemsigdb.
An ExperimentHub Package for the Molecular Signatures Database (MSigDB)
Bioconductor version: Release (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("msigdb")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("msigdb")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text |
Details
| biocViews | ExperimentData,ExperimentHub,Homo_sapiens_Data,Mus_musculus_Data |
| Version | 1.18.0 |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | msigdb_1.18.0.tar.gz |
| Windows Binary (x86_64) | |
| 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/ |
| Package Downloads Report | Download Stats |