{ "_id": "6a153368acfb0bcc41d4ee10", "Package": "MSTree", "Title": "MSTree plotting minimum spanning tree directly from the output\nof ChewBBACA pipeline", "Version": "0.99.6", "Authors@R": "person(\"Abdullah\", \"El-Kurdi\", , \"ak161@aub.edu.lb\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-8321-4025\"))", "Description": "This package is used to generate a graph object from the\noutput of chewBBACA pipeline\n(https://chewbbaca.readthedocs.io/en/latest/). Then, the\ngenerated graph object can be used to make a minimum spanning\ntree (MST). The minimum spanning tree can be customized using\nall the available arguments. This package consists of two\nfunctions: one to build the graph and another one for plotting.", "License": "Artistic-2.0", "biocViews": "ComparativeGenomics, GenomicVariation, Clustering", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.1", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libfontconfig1-dev libfreetype6-dev libglpk-dev\nlibicu-dev libxml2-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-05-15 10:44:33 UTC", "RemoteUrl": "https://github.com/bioc/MSTree", "RemoteRef": "HEAD", "RemoteSha": "08cdc1833921fa67b40aaaa275cd641f8a8f02e0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-24 15:04:54 UTC", "User": "root" }, "Author": "Abdullah El-Kurdi [aut, cre] (ORCID:\n)", "Maintainer": "Abdullah El-Kurdi ", "MD5sum": "33465c0cb2b8e3d6db885a8a75a4dce4", "_user": "bioc", "_type": "src", "_file": "MSTree_0.99.6.tar.gz", "_fileid": "9e47f99e6dfa6cb0e0e5ba0c3fa50c4e8a0b759943210f79b7a850f3d9d379c5", "_filesize": 115532, "_sha256": "9e47f99e6dfa6cb0e0e5ba0c3fa50c4e8a0b759943210f79b7a850f3d9d379c5", "_created": "2026-05-24T15:04:54.000Z", "_published": "2026-05-26T05:45:12.465Z", "_jobs": [ { "job": 77814562652, "time": 157, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7186144261" }, { "job": 77814562797, "time": 341, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7186163645" }, { "job": 77814562737, "time": 273, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7186156473" }, { "job": 77814562735, "time": 90, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7186137437" }, { "job": 77814562670, "time": 105, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7186138902" }, { "job": 77814562371, "time": 206, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7186127666" }, { "job": 77814562715, "time": 135, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7186141971" }, { "job": 77814562471, "time": 94, "config": "windows-devel", "r": "4.7.0", "check": "FAIL", "artifact": "" }, { "job": 77814562449, "time": 104, "config": "windows-oldrel", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 77814562447, "time": 96, "config": "windows-release", "r": "4.6.0", "check": "FAIL", "artifact": "" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26364642969", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/MSTree", "_commit": { "id": "08cdc1833921fa67b40aaaa275cd641f8a8f02e0", "author": "abedkurdi ", "committer": "abedkurdi ", "message": "pushing 0.99.7 typos correction\n", "time": 1778841873 }, "_maintainer": { "name": "Abdullah El-Kurdi", "email": "ak161@aub.edu.lb", "orcid": "0000-0002-8321-4025" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "igraph", "role": "Imports" }, { "package": "ggraph", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "NetPathMiner", "role": "Imports" }, { "package": "RUnit", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-07", "n": 12 }, { "week": "2026-10", "n": 6 }, { "week": "2026-20", "n": 5 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "0.99.6", "bioc": "3.24" } ], "_topics": [ "comparativegenomics", "genomicvariation", "clustering" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MSTree.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "makeGraphFromChewBBACA", "PlotMST" ], "_help": [ { "page": "makeGraphFromChewBBACA", "title": "MSTree R package", "topics": [ "makeGraphFromChewBBACA" ] }, { "page": "PlotMST", "title": "MSTree R package", "topics": [ "PlotMST" ] } ], "_rundeps": [ "base64enc", "cachem", "cli", "cpp11", "dplyr", "farver", "fastmap", "generics", "ggforce", "ggplot2", "ggraph", "ggrepel", "glue", "graphlayouts", "gridExtra", "gtable", "igraph", "isoband", "jsonlite", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "memoise", "NetPathMiner", "pillar", "pkgconfig", "polyclip", "purrr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "rlang", "S7", "scales", "stringi", "stringr", "systemfonts", "tibble", "tidygraph", "tidyr", "tidyselect", "tweenr", "utf8", "vctrs", "viridis", "viridisLite", "withr" ], "_vignettes": [ { "source": "MSTree_vignette.Rmd", "filename": "MSTree_vignette.html", "title": "MSTree: Building Minimum Spanning Tree (MST) from chewBBACA pipeline output", "author": "Abdullah El-Kurdi", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Overview", "Example", "Session information" ], "created": "2026-02-09 07:58:21", "modified": "2026-05-11 13:29:35", "commits": 8 } ], "_score": 3.4771212547196626, "_indexed": true, "_nocasepkg": "mstree", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.6", "date": "2026-05-24T15:10:05.000Z", "distro": "noble", "commit": "08cdc1833921fa67b40aaaa275cd641f8a8f02e0", "fileid": "6c2857522e508b9bbac03fbaeeef9d5e438b6e3d26b5302391da5ed2963b8672", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26364642969" }, { "r": "4.6.0", "os": "linux", "version": "0.99.6", "date": "2026-05-24T15:08:55.000Z", "distro": "noble", "commit": "08cdc1833921fa67b40aaaa275cd641f8a8f02e0", "fileid": "c3cc60be814985c057ee0d3b08dcde90b49f219fa3698e278e04e127aafd97d8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26364642969" }, { "r": "4.5.3", "os": "mac", "version": "0.99.6", "date": "2026-05-24T15:06:14.000Z", "commit": "08cdc1833921fa67b40aaaa275cd641f8a8f02e0", "fileid": "df58ac97029494a50ce669129c4f23e5a82b0b4beccfd4783c7d46415a7affd9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26364642969" }, { "r": "4.6.0", "os": "mac", "version": "0.99.6", "date": "2026-05-24T15:06:22.000Z", "commit": "08cdc1833921fa67b40aaaa275cd641f8a8f02e0", "fileid": "e505abc3b69ab607b708f69ab1b954bffe0e6f37c44f071537d814bcf2e78ed7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26364642969" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.6", "date": "2026-05-24T15:07:26.000Z", "commit": "08cdc1833921fa67b40aaaa275cd641f8a8f02e0", "fileid": "9246c223998559456873af305cfd809b44b973198649cd1b90487d74328a9e33", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26364642969" } ] }