msigdb
An ExperimentHub Package for the Molecular Signatures Database (MSigDB)
Bioconductor version: 3.23 · Package version: 1.20.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("msigdb")Details
| Maintainer | Dharmesh D. Bhuva <bhuva.d@wehi.edu.au> |
| Author | Dharmesh D. Bhuva [aut, cre] (ORCID: <https://orcid.org/0000-0002-6398-9157>), Gordon K. Smyth [aut] (ORCID: <https://orcid.org/0000-0001-9221-2892>), Alexandra Garnham [aut] (ORCID: <https://orcid.org/0000-0002-8312-8450>) |
| License | CC BY 4.0 |
| URL | https://davislaboratory.github.io/msigdb |
| Bug Reports | https://github.com/DavisLaboratory/msigdb/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ExperimentData, ExperimentHub, Homo_sapiens_Data, Mus_musculus_Data |
| Package Short Url | https://bioconductor.org/packages/msigdb/ |
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 1.20.0, https://bioconductor.org/packages/msigdb.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | msigdb_1.20.0.tar.gz |
Dependencies
Depends: R (>= 4.1)
Imports: ExperimentHub, utils, GSEABase, org.Mm.eg.db, org.Hs.eg.db, AnnotationDbi, methods, stats, AnnotationHub
Suggests: singscore, vissE, knitr, prettydoc, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocFileCache, GO.db, stringr, limma