The Molecular Signatures Database (MSigDB) | Download data from the msigdb R package | Downloading and integrating KEGG gene sets | Accessing the GeneSet and GeneSetCollection objects | Subset collections from the MSigDB | Preparing collections for limma::fry | Accessing the mouse MSigDB | Session information
Package: msigdb 1.20.0
Dharmesh D. Bhuva
msigdb: An ExperimentHub Package for the Molecular Signatures Database (MSigDB)
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.
Authors:
msigdb_1.20.0.tar.gz
msigdb_1.20.0.tar.gz(r-4.7-any)msigdb_1.20.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
msigdb/json (API)
| # Install 'msigdb' in R: |
| install.packages('msigdb', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/davislaboratory/msigdb/issues
On BioConductor:msigdb-1.21.0(data/experiment 3.24)msigdb-1.20.0(data/experiment 3.23)
experimenthubhomo_sapiens_datamus_musculus_datadatapkg
Last updated from:e6db46ce88 (on RELEASE_3_23). Checks:3 WARNING, 1 OK. Indexed: no.
This is a data package. Data packages may be large and do not get checked across all platforms.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 198 | ||
| linux-devel | WARNING | 1457 | ||
| source / vignettes | OK | 401 | ||
| linux-release | WARNING | 1323 |
Exports:appendKEGGgetIMEXgetIMEXVersionsgetMsigdbgetMsigdbIDFgetMsigdbVersionsgetMsigIdTypegetMsigOrganismlistCollectionslistSubCollectionssubsetCollection
Dependencies:annotateAnnotationDbiAnnotationHubaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdplyrExperimentHubfastmapfilelockgenericsgluegraphGSEABasehttrhttr2IRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslorg.Hs.eg.dborg.Mm.eg.dbpillarpkgconfigpngpurrrR6rappdirsrlangRSQLiteS4VectorsSeqinfostringistringrsystibbletidyrtidyselectutf8vctrswithrXMLxtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add KEGG pathway derived gene sets to a collection | appendKEGG |
| Retrieve IMEx PPI hosted on the hub | getIMEX |
| Get IMEX versions included in the msigdb package | getIMEXVersions |
| Retrieve MSigDB data hosted on the hub | getMsigdb |
| Retrieve MSigDB data hosted on the hub | getMsigdbIDF |
| Get MSigDB versions included in the msigdb package | getMsigdbVersions |
| Infer gene identifier type for the gene set collection | getMsigIdType |
| Infer organism type for the gene set collection | getMsigOrganism |
| List all collection types within a MSigDB gene set collection | listCollections |
| List all sub-collection types within a MSigDB gene set collection | listSubCollections |
| The Molecular Signatures Database (MSigDB) | msigdb-package msigdb |
| Subset collections and sub-collections of MSigDB | subsetCollection |