{ "_id": "6a1957a6acfb0bcc41de2b85", "Package": "bugphyzz", "Title": "A harmonized data resource and software for enrichment analysis\nof microbial physiologies", "Version": "1.7.1", "Authors@R": "c(\nperson(\"Samuel\", \"Gamboa\", , \"Samuel.Gamboa.Tuz@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-6863-7943\")),\nperson(\"Levi\", \"Waldron\", , \"levi.waldron@sph.cuny.edu\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-2725-0694\")),\nperson(\"Kelly\", \"Eckenrode\", role = \"aut\"),\nperson(\"Jonathan\", \"Ye\", role = \"aut\"),\nperson(\"Jennifer\", \"Wokaty\", role = \"aut\"),\nperson(\"NCI\", role = \"fnd\",\ncomment = c(GrantNo. = \"R01CA230551\"))\n)", "Description": "bugphyzz is an electronic database of standardized\nmicrobial annotations. It facilitates the creation of microbial\nsignatures based on shared attributes, which are utilized for\nbug set enrichment analysis. The data also includes annotations\nimputed with ancestra state reconstruction methods.", "biocViews": "MicrobiomeData, ReproducibleResearch", "License": "Artistic-2.0", "Config/testthat/edition": "3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.1", "VignetteBuilder": "knitr", "URL": "https://github.com/waldronlab/bugphyzz", "BugReports": "https://github.com/waldronlab/bugphyzz/issues", "Config/pak/sysreqs": "libicu-dev libssl-dev", "Repository": "https://waldronlab.r-universe.dev", "Date/Publication": "2026-04-29 21:16:59 UTC", "RemoteUrl": "https://github.com/waldronlab/bugphyzz", "RemoteRef": "HEAD", "RemoteSha": "7b909fe05f2ee2f2ea1e6b09ebfc702c006504f2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 07:59:29 UTC", "User": "root" }, "Author": "Samuel Gamboa [aut, cre] (ORCID:\n),\nLevi Waldron [aut] (ORCID: ),\nKelly Eckenrode [aut],\nJonathan Ye [aut],\nJennifer Wokaty [aut],\nNCI [fnd] (GrantNo.: R01CA230551)", "Maintainer": "Samuel Gamboa ", "MD5sum": "9583603f821e66f934ff6e62ac89897c", "_user": "waldronlab", "_type": "src", "_file": "bugphyzz_1.7.1.tar.gz", "_fileid": "7e9ba7c5f5c0a878b088df749550fea4fea867fc38f2c94b311525e76f109851", "_filesize": 786552, "_sha256": "7e9ba7c5f5c0a878b088df749550fea4fea867fc38f2c94b311525e76f109851", "_created": "2026-05-29T07:59:29.000Z", "_published": "2026-05-29T09:08:54.228Z", "_distro": "noble", "_jobs": [ { "job": 78461496721, "time": 444, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7286054512" }, { "job": 78461496712, "time": 543, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7286081429" }, { "job": 78461496786, "time": 490, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7287142771" }, { "job": 78461496734, "time": 388, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7287108908" }, { "job": 78460639781, "time": 372, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7285930080" }, { "job": 78461496730, "time": 213, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7285989959" }, { "job": 78461496753, "time": 448, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7286056068" }, { "job": 78461496742, "time": 476, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7286063165" }, { "job": 78461496764, "time": 482, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7286065121" } ], "_buildurl": "https://github.com/r-universe/waldronlab/actions/runs/26625337022", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/waldronlab/bugphyzz", "_commit": { "id": "7b909fe05f2ee2f2ea1e6b09ebfc702c006504f2", "author": "LiNk-NY ", "committer": "LiNk-NY ", "message": "version bump 1.7.1\n", "time": 1777497419 }, "_maintainer": { "name": "Samuel Gamboa", "email": "samuel.gamboa.tuz@gmail.com", "login": "sdgamboa", "orcid": "0000-0002-6863-7943", "description": "\n", "uuid": 53412049 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "tidyselect", "role": "Imports" }, { "package": "BiocFileCache", "role": "Imports" }, { "package": "httr2", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "DT", "role": "Suggests" }, { "package": "forcats", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "htmltools", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "sessioninfo", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "EnrichmentBrowser", "role": "Suggests" }, { "package": "MicrobiomeBenchmarkData", "role": "Suggests" }, { "package": "mia", "role": "Suggests" }, { "package": "stats", "role": "Suggests" }, { "package": "rlang", "role": "Suggests" }, { "package": "limma", "role": "Suggests" }, { "package": "mgsub", "role": "Suggests" }, { "package": "methods", "role": "Suggests" }, { "package": "readr", "role": "Suggests" }, { "package": "crayon", "role": "Suggests" }, { "package": "tibble", "role": "Suggests" }, { "package": "magrittr", "role": "Suggests" }, { "package": "tidytext", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "waldronlab", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 4 } ], "_tags": [], "_topics": [ "microbiomedata", "reproducibleresearch", "r01ca230551" ], "_stars": 6, "_contributors": [ { "user": "sdgamboa", "count": 652, "uuid": 53412049 }, { "user": "kbeckenrode", "count": 175, "uuid": 16803526 }, { "user": "lwaldron", "count": 46, "uuid": 639942 }, { "user": "jonathanye3", "count": 44, "uuid": 66918590 }, { "user": "jwokaty", "count": 26, "uuid": 1744257 }, { "user": "lshep", "count": 8, "uuid": 18724380 }, { "user": "link-ny", "count": 2, "uuid": 4392950 }, { "user": "jananiravi", "count": 1, "uuid": 8397074 } ], "_userbio": { "uuid": 15236403, "type": "organization", "name": "Waldron Lab at the CUNY SPH", "description": "Software and educational materials from the Waldron lab for computational biostatistics at the CUNY SPH in New York City" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/bugphyzz" }, "_devurl": "https://github.com/waldronlab/bugphyzz", "_searchresults": 32, "_rbuild": "4.6.0", "_assets": [ "extra/bugphyzz.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" ], "_cranurl": false, "_exports": [ "getTaxonSignatures", "importBugphyzz", "makeSignatures", "physiologies", "showPhys" ], "_help": [ { "page": "getTaxonSignatures", "title": "Get Taxon Signatures", "topics": [ "getTaxonSignatures" ] }, { "page": "importBugphyzz", "title": "Import bugphyzz", "topics": [ "importBugphyzz" ] }, { "page": "makeSignatures", "title": "Make signatures", "topics": [ "makeSignatures" ] }, { "page": "physiologies", "title": "Import physiologies (for devs)", "topics": [ "physiologies" ] }, { "page": "showPhys", "title": "Show list of available physiologies (for devs)", "topics": [ "showPhys" ] } ], "_readme": "https://github.com/waldronlab/bugphyzz/raw/HEAD/README.md", "_rundeps": [ "askpass", "BiocFileCache", "BiocGenerics", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "curl", "DBI", "dbplyr", "dplyr", "fastmap", "filelock", "generics", "glue", "httr2", "lifecycle", "magrittr", "memoise", "openssl", "pillar", "pkgconfig", "purrr", "R6", "rappdirs", "rlang", "RSQLite", "S4Vectors", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr" ], "_vignettes": [ { "source": "bugphyzz.Rmd", "filename": "bugphyzz.html", "title": "bugphyzz", "author": "Samuel Gamboa, Levi Waldron", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Data schema", "Analysis and Stats", "Installation", "Import bugphyzz data", "Create microbial signatures", "Run a bug set enrichment analysis", "Get signatures associated with a specific microbe", "Session information" ], "created": "2021-09-18 00:42:40", "modified": "2024-06-27 21:34:00", "commits": 37 }, { "source": "sources.Rmd", "filename": "sources.html", "title": "Sources", "engine": "knitr::rmarkdown", "headings": [ "Sources" ], "created": "2024-06-27 21:34:00", "modified": "2024-06-27 21:34:00", "commits": 1 } ], "_score": 5.429429264381787, "_indexed": true, "_nocasepkg": "bugphyzz", "_universes": [ "waldronlab", "sdgamboa" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.7.1", "date": "2026-05-29T08:02:39.000Z", "distro": "noble", "commit": "7b909fe05f2ee2f2ea1e6b09ebfc702c006504f2", "fileid": "c3130431cf90048b740d58ef88067472b0473127bc5a4d75c9a7640c318ff20c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/26625337022" }, { "r": "4.6.0", "os": "linux", "version": "1.7.1", "date": "2026-05-29T08:03:13.000Z", "distro": "noble", "commit": "7b909fe05f2ee2f2ea1e6b09ebfc702c006504f2", "fileid": "c990111d3181e374e95cf5226baec93c6e7dc83ffa0c64d6c032c671f12f9b5d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/26625337022" }, { "r": "4.5.3", "os": "mac", "version": "1.7.1", "date": "2026-05-29T09:04:13.000Z", "commit": "7b909fe05f2ee2f2ea1e6b09ebfc702c006504f2", "fileid": "1f00839f4b0482808e44586e203e93e087829869ba08716a9743769f216228f4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/26625337022" }, { "r": "4.6.0", "os": "mac", "version": "1.7.1", "date": "2026-05-29T09:01:50.000Z", "commit": "7b909fe05f2ee2f2ea1e6b09ebfc702c006504f2", "fileid": "850fcfaaa2f322d837d8c55f1aa2105acc9c180013a1775662a70a8d31effe8d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/26625337022" }, { "r": "4.6.0", "os": "wasm", "version": "1.7.1", "date": "2026-05-29T08:03:14.000Z", "commit": "7b909fe05f2ee2f2ea1e6b09ebfc702c006504f2", "fileid": "305095da5d80996c815fae2b1c37818ac4ab9f998d425574ed923cd95f000e5b", "status": "success", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/26625337022" }, { "r": "4.7.0", "os": "win", "version": "1.7.1", "date": "2026-05-29T08:01:46.000Z", "commit": "7b909fe05f2ee2f2ea1e6b09ebfc702c006504f2", "fileid": "55931c472662de79bb03e1ab656f4c77b78cc1e0693be9daf23b5ed9ff2a273f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/26625337022" }, { "r": "4.5.3", "os": "win", "version": "1.7.1", "date": "2026-05-29T08:01:39.000Z", "commit": "7b909fe05f2ee2f2ea1e6b09ebfc702c006504f2", "fileid": "c2011a25a38367e6498fb02c0bc3768e53ca55ddfc8a0902bde908788b0275f2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/26625337022" }, { "r": "4.6.0", "os": "win", "version": "1.7.1", "date": "2026-05-29T08:01:49.000Z", "commit": "7b909fe05f2ee2f2ea1e6b09ebfc702c006504f2", "fileid": "10fa4a034e4008bc72a2a48903ea310fc33bfc7a13e900e54bd954a705f53b84", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/26625337022" } ] }