{ "_id": "6a12aa4bacfb0bcc41d16c92", "Package": "bugsigdbr", "Version": "1.18.0", "Title": "R-side access to published microbial signatures from BugSigDB", "Authors@R": "c(\nperson(\"Ludwig\", \"Geistlinger\", , \"ludwig.geistlinger@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Jennifer\", \"Wokaty\", , \"jennifer.wokaty@sph.cuny.edu\", role = \"aut\"),\nperson(\"Levi\", \"Waldron\", , \"lwaldron.research@gmail.com\", role = \"aut\"),\nperson(\"NCI\", role = \"fnd\",\ncomment = c(GrantNo. = \"R01CA230551\"))\n)", "Description": "The bugsigdbr package implements convenient access to\nbugsigdb.org from within R/Bioconductor. The goal of the\npackage is to facilitate import of BugSigDB data into\nR/Bioconductor, provide utilities for extracting microbe\nsignatures, and enable export of the extracted signatures to\nplain text files in standard file formats such as GMT.", "URL": "https://github.com/waldronlab/bugsigdbr", "BugReports": "https://github.com/waldronlab/bugsigdbr/issues", "License": "GPL-3", "VignetteBuilder": "knitr", "biocViews": "DataImport, GeneSetEnrichment, Metagenomics, Microbiome", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libicu-dev libssl-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:56:47 UTC", "RemoteUrl": "https://github.com/bioc/bugsigdbr", "RemoteRef": "RELEASE_3_23", "RemoteSha": "2196252e42db2152ae0ab99ad3ef9d42973832dd", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-24 06:42:42 UTC", "User": "root" }, "Author": "Ludwig Geistlinger [aut, cre],\nJennifer Wokaty [aut],\nLevi Waldron [aut],\nNCI [fnd] (GrantNo.: R01CA230551)", "Maintainer": "Ludwig Geistlinger ", "MD5sum": "eb097336a297ab32deff124c3f0e21b2", "_user": "bioc-release", "_type": "src", "_file": "bugsigdbr_1.18.0.tar.gz", "_fileid": "f5226c099779e1d32c3af78b95eacb8daeeaadcc07294c446eeab629eb9c5527", "_filesize": 166659, "_sha256": "f5226c099779e1d32c3af78b95eacb8daeeaadcc07294c446eeab629eb9c5527", "_created": "2026-05-24T06:42:42.000Z", "_published": "2026-05-24T07:35:39.467Z", "_jobs": [ { "job": 77578041447, "time": 145, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7182976817" }, { "job": 77578041451, "time": 366, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7182998706" }, { "job": 77578041457, "time": 354, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7182997589" }, { "job": 77578041456, "time": 256, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7183305715" }, { "job": 77578041452, "time": 293, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7183293996" }, { "job": 77577827379, "time": 260, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7182962072" }, { "job": 77578041449, "time": 113, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7182973569" }, { "job": 77578041472, "time": 264, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7182988778" }, { "job": 77578041477, "time": 298, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7182992128" }, { "job": 77578041461, "time": 252, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7182987590" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354196799", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/bugsigdbr", "_commit": { "id": "2196252e42db2152ae0ab99ad3ef9d42973832dd", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777381007 }, "_maintainer": { "name": "Ludwig Geistlinger", "email": "ludwig.geistlinger@gmail.com", "login": "lgeistlinger", "description": "", "uuid": 11871050 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "BiocFileCache", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "vroom", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "ontologyIndex", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-22", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2025-51", "n": 1 }, { "week": "2026-01", "n": 1 }, { "week": "2026-15", "n": 2 }, { "week": "2026-17", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.19.0", "bioc": "3.24" }, { "branch": "release", "version": "1.18.0", "bioc": "3.23" } ], "_topics": [ "dataimport", "genesetenrichment", "metagenomics", "microbiome", "bioconductor-package", "r01ca230551" ], "_stars": 6, "_contributors": [ { "user": "jwokaty", "count": 71, "uuid": 1744257 }, { "user": "lgeistlinger", "count": 69, "uuid": 11871050 }, { "user": "lwaldron", "count": 11, "uuid": 639942 }, { "user": "nturaga", "count": 4, "uuid": 2746443 }, { "user": "link-ny", "count": 3, "uuid": 4392950 }, { "user": "cmirzayi", "count": 2, "uuid": 13036789 }, { "user": "lshep", "count": 1, "uuid": 18724380 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 854, "source": "https://www.bioconductor.org/packages/stats/bioc/bugsigdbr" }, "_devurl": "https://github.com/waldronlab/bugsigdbr", "_searchresults": 65, "_rbuild": "4.6.0", "_assets": [ "extra/bugsigdbr.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/waldronlab/bugsigdbr", "_realowner": "bioc", "_cranurl": false, "_exports": [ "browseSignature", "browseTaxon", "extractTaxLevel", "getMetaSignatures", "getOntology", "getSignatures", "importBugSigDB", "restrictTaxLevel", "subsetByOntology", "writeGMT" ], "_help": [ { "page": "browseSignature", "title": "Displaying BugSigDB signatures pages in a web browser", "topics": [ "browseSignature" ] }, { "page": "browseTaxon", "title": "Displaying BugSigDB taxon pages in a web browser", "topics": [ "browseTaxon" ] }, { "page": "extractTaxLevel", "title": "Extract specific taxonomic levels from a microbe signature", "topics": [ "extractTaxLevel" ] }, { "page": "getMetaSignatures", "title": "Obtain meta-signatures for a column of interest", "topics": [ "getMetaSignatures" ] }, { "page": "getOntology", "title": "Obtain the EFO and UBERON ontology", "topics": [ "getOntology" ] }, { "page": "getSignatures", "title": "Obtain microbe signatures from BugSigDB", "topics": [ "getSignatures" ] }, { "page": "importBugSigDB", "title": "Obtain published microbial signatures from bugsigdb.org", "topics": [ "importBugSigDB" ] }, { "page": "restrictTaxLevel", "title": "Restrict microbe signatures to specific taxonomic levels", "topics": [ "restrictTaxLevel" ] }, { "page": "subsetByOntology", "title": "Ontology-based subsetting of BugSigDB signatures", "topics": [ "subsetByOntology" ] }, { "page": "writeGMT", "title": "Write microbe signatures to file in GMT format", "topics": [ "writeGMT" ] } ], "_readme": "https://github.com/bioc/bugsigdbr/raw/RELEASE_3_23/README.md", "_rundeps": [ "askpass", "BiocFileCache", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "crayon", "curl", "DBI", "dbplyr", "dplyr", "fastmap", "filelock", "generics", "glue", "hms", "httr2", "lifecycle", "magrittr", "memoise", "openssl", "pillar", "pkgconfig", "prettyunits", "progress", "purrr", "R6", "rappdirs", "rlang", "RSQLite", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "tzdb", "utf8", "vctrs", "vroom", "withr" ], "_vignettes": [ { "source": "bugsigdbr.Rmd", "filename": "bugsigdbr.html", "title": "R-side access to published microbial signatures from BugSigDB", "author": "Ludwig Geistlinger, Jennifer Wokaty, and Levi Waldron", "engine": "knitr::rmarkdown", "headings": [ "BugSigDB: a comprehensive database of published microbial signatures", "Obtaining published microbial signatures from BugSigDB", "Extracting microbe signatures", "Writing microbe signatures to file in GMT format", "Displaying BugSigDB signature and taxon pages", "Ontology-based queries for experimental factors and body sites", "Session info" ], "created": "2021-04-05 19:31:14", "modified": "2025-12-29 13:57:03", "commits": 13 } ], "_score": 6.913283901760418, "_indexed": false, "_nocasepkg": "bugsigdbr", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/bugsigdbr", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.18.0", "date": "2026-05-24T06:45:39.000Z", "distro": "noble", "commit": "2196252e42db2152ae0ab99ad3ef9d42973832dd", "fileid": "8252e16222bd23c71d318bcb80363a1bab613eb474e51c2766d0a0ff5acc7feb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354196799" }, { "r": "4.6.0", "os": "linux", "version": "1.18.0", "date": "2026-05-24T06:45:44.000Z", "distro": "noble", "commit": "2196252e42db2152ae0ab99ad3ef9d42973832dd", "fileid": "f60c5fc9b9de046f3fb686a7e7f51340b883b97da180867e19d4f0921ef7e9db", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354196799" }, { "r": "4.5.3", "os": "mac", "version": "1.18.0", "date": "2026-05-24T07:32:19.000Z", "commit": "2196252e42db2152ae0ab99ad3ef9d42973832dd", "fileid": "b8e58984240b6c5941381abab762363ef8222b86c5ba00fb6fdfd9c748276a76", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354196799" }, { "r": "4.6.0", "os": "mac", "version": "1.18.0", "date": "2026-05-24T07:30:11.000Z", "commit": "2196252e42db2152ae0ab99ad3ef9d42973832dd", "fileid": "0d6a68ef88834ec41a4bf3ec0c760a1b32c6e474a8f7fad1b3b06adad1a2db41", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354196799" }, { "r": "4.6.0", "os": "wasm", "version": "1.18.0", "date": "2026-05-24T06:44:50.000Z", "commit": "2196252e42db2152ae0ab99ad3ef9d42973832dd", "fileid": "d82573a830e5faffbf55cc84d3485b2230020adb20261408a718b601b0c2aae2", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354196799" }, { "r": "4.7.0", "os": "win", "version": "1.18.0", "date": "2026-05-24T06:44:01.000Z", "commit": "2196252e42db2152ae0ab99ad3ef9d42973832dd", "fileid": "eb7e1cfc417f8dbb5cb8dcec51965e5c83e9228d1a13e62b2621bb745318b023", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354196799" }, { "r": "4.5.3", "os": "win", "version": "1.18.0", "date": "2026-05-24T06:43:58.000Z", "commit": "2196252e42db2152ae0ab99ad3ef9d42973832dd", "fileid": "c6f2c0211116613ed9efd9c674498c9f111e850571b6f413824f15b70d6b4841", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354196799" }, { "r": "4.6.0", "os": "win", "version": "1.18.0", "date": "2026-05-24T06:43:48.000Z", "commit": "2196252e42db2152ae0ab99ad3ef9d42973832dd", "fileid": "517c0d64c01af91da0cdfd1919ebe116ce3f5c920629c819071ab8628086eb2b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354196799" } ] }