{ "_id": "6aca24c8fe5cc25786e850ce", "Package": "msigdb", "Title": "An ExperimentHub Package for the Molecular Signatures Database\n(MSigDB)", "Version": "1.20.0", "Authors@R": "c(\nperson(given = \"Dharmesh D.\",\nfamily = \"Bhuva\",\nrole = c(\"aut\", \"cre\"),\nemail = \"bhuva.d@wehi.edu.au\",\ncomment = c(ORCID = \"0000-0002-6398-9157\")),\nperson(given = \"Gordon K.\",\nfamily = \"Smyth\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0001-9221-2892\")),\nperson(given = \"Alexandra\",\nfamily = \"Garnham\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-8312-8450\"))\n)", "Description": "This package provides the Molecular Signatures Database\n(MSigDB) in a R accessible objects. Signatures are stored in\nGeneSet class objects form the GSEABase package and the entire\ndatabase is stored in a GeneSetCollection object. These data\nare then hosted on the ExperimentHub. Data used in this package\nwas obtained from the MSigDB of the Broad Institute. Metadata\nfor each gene set is stored along with the gene set in the\nGeneSet class object.", "biocViews": "ExperimentHub, Homo_sapiens_Data, Mus_musculus_Data", "License": "CC BY 4.0", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "URL": "https://davislaboratory.github.io/msigdb", "BugReports": "https://github.com/DavisLaboratory/msigdb/issues", "NeedsCompilation": "no", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libicu-dev libpng-dev libxml2-dev libssl-dev\nzlib1g-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:35:19 UTC", "RemoteUrl": "https://github.com/bioc/msigdb", "RemoteRef": "RELEASE_3_23", "RemoteSha": "e6db46ce8891e6a0099dd95c482a0f5c701b9399", "Packaged": { "Date": "2026-10-10 11:18:14 UTC", "User": "root" }, "Author": "Dharmesh D. Bhuva [aut, cre] (ORCID:\n),\nGordon K. Smyth [aut] (ORCID: ),\nAlexandra Garnham [aut] (ORCID:\n)", "Maintainer": "Dharmesh D. Bhuva ", "_user": "bioc-release", "_type": "src", "_file": "msigdb_1.20.0.tar.gz", "_fileid": "https://r2.ropensci.org/11b47c1948ea4bf4558d6f3952019e41c468bbb16f73df8d7fefc76b7e61904f", "_filesize": 369359, "_sha256": "11b47c1948ea4bf4558d6f3952019e41c468bbb16f73df8d7fefc76b7e61904f", "_expires": "2027-01-18T11:43:02.000Z", "_created": "2026-10-10T11:18:14.000Z", "_published": "2026-10-10T11:43:04.470Z", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047529999", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 1, "note": 10 }, "_upstream": "https://github.com/bioc/msigdb", "_commit": { "id": "e6db46ce8891e6a0099dd95c482a0f5c701b9399", "author": "lshep ", "committer": "lshep ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379719 }, "_maintainer": { "name": "Dharmesh D. Bhuva", "email": "bhuva.d@wehi.edu.au", "orcid": "0000-0002-6398-9157" }, "_distro": "resolute", "_jobs": [ { "job": 114201153115, "time": 198, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "11667928069" }, { "job": 114201153078, "time": 1457, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11668827477" }, { "job": 114201153099, "time": 1323, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11668577679" }, { "job": 114200018809, "time": 401, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11668107552" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "ExperimentHub", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "GSEABase", "role": "Imports" }, { "package": "org.Mm.eg.db", "role": "Imports" }, { "package": "org.Hs.eg.db", "role": "Imports" }, { "package": "AnnotationDbi", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "AnnotationHub", "role": "Imports" }, { "package": "singscore", "role": "Suggests" }, { "package": "vissE", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "prettydoc", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "BiocFileCache", "role": "Suggests" }, { "package": "GO.db", "role": "Suggests" }, { "package": "stringr", "role": "Suggests" }, { "package": "limma", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 4, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24", "repository": "data/experiment" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23", 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"_exports": [ "appendKEGG", "getIMEX", "getIMEXVersions", "getMsigdb", "getMsigdbIDF", "getMsigdbVersions", "getMsigIdType", "getMsigOrganism", "listCollections", "listSubCollections", "subsetCollection" ], "_help": [ { "page": "appendKEGG", "title": "Add KEGG pathway derived gene sets to a collection", "topics": [ "appendKEGG" ] }, { "page": "getIMEX", "title": "Retrieve IMEx PPI hosted on the hub", "topics": [ "getIMEX" ] }, { "page": "getIMEXVersions", "title": "Get IMEX versions included in the msigdb package", "topics": [ "getIMEXVersions" ] }, { "page": "getMsigdb", "title": "Retrieve MSigDB data hosted on the hub", "topics": [ "getMsigdb" ] }, { "page": "getMsigdbIDF", "title": "Retrieve MSigDB data hosted on the hub", "topics": [ "getMsigdbIDF" ] }, { "page": "getMsigdbVersions", "title": "Get MSigDB versions included in the msigdb package", "topics": [ "getMsigdbVersions" ] }, { "page": "getMsigIdType", "title": "Infer gene identifier type for the gene set collection", "topics": [ "getMsigIdType" ] }, { "page": "getMsigOrganism", "title": "Infer organism type for the gene set collection", "topics": [ "getMsigOrganism" ] }, { "page": "listCollections", "title": "List all collection types within a MSigDB gene set collection", "topics": [ "listCollections" ] }, { "page": "listSubCollections", "title": "List all sub-collection types within a MSigDB gene set collection", "topics": [ "listSubCollections" ] }, { "page": "msigdb", "title": "The Molecular Signatures Database (MSigDB)", "topics": [ "msigdb-package", "msigdb" ] }, { "page": "subsetCollection", "title": "Subset collections and sub-collections of MSigDB", "topics": [ "subsetCollection" ] } ], "_readme": "https://github.com/bioc/msigdb/raw/RELEASE_3_23/README.md", "_rundeps": [ "annotate", "AnnotationDbi", "AnnotationHub", "askpass", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocManager", "BiocVersion", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "crayon", "curl", "DBI", "dbplyr", "dplyr", "ExperimentHub", "fastmap", "filelock", "generics", "glue", "graph", "GSEABase", "httr", "httr2", "IRanges", "jsonlite", "KEGGREST", "lifecycle", "magrittr", "memoise", "mime", "openssl", "org.Hs.eg.db", "org.Mm.eg.db", "pillar", "pkgconfig", "png", "purrr", "R6", "rappdirs", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "XML", "xtable", "XVector", "yaml" ], "_vignettes": [ { "source": "msigdb.Rmd", "filename": "msigdb.html", "title": "msigdb: The molecular signatures database (MSigDB) in R", "author": "Dharmesh D. Bhuva", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2021-05-10 02:09:54", "modified": "2022-01-17 23:40:44", "commits": 3 } ], "_score": 7.480581786829169, "_indexed": false, "_nocasepkg": "msigdb", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/msigdb", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.20.0", "date": "2026-10-10T11:23:08.000Z", "distro": "resolute", "commit": "e6db46ce8891e6a0099dd95c482a0f5c701b9399", "fileid": "https://r2.ropensci.org/a00f2ecc76de400a67d078ad5d9744d0ce199fa567af87a0c2a6c6e579805f5d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047529999" }, { "r": "4.6.1", "os": "linux", "version": "1.20.0", "date": "2026-10-10T11:23:09.000Z", "distro": "resolute", "commit": "e6db46ce8891e6a0099dd95c482a0f5c701b9399", "fileid": "https://r2.ropensci.org/c9242984fdba5e6833add6fd2184003fc7cbd512333276ad6d4bb56175c61720", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047529999" } ] }