{
  "_id": "6a196c9eacfb0bcc41deac7a",
  "Package": "barbieQ",
  "Type": "Package",
  "Title": "Analyze Barcode Data from Clonal Tracking Experiments",
  "Version": "1.5.0",
  "Description": "The barbieQ package provides a series of robust\nstatistical tools for analysing barcode count data generated\nfrom cell clonal tracking (i.e., lineage tracing) experiments.\nIn these experiments, an initial cell and its offspring\ncollectively form a clone (i.e., lineage). A unique barcode\nsequence, incorporated into the DNA of the inital cell, is\ninherited within the clone. This one-to-one mapping of barcodes\nto clones enables clonal tracking of their behaviors. By\ncounting barcodes, researchers can quantify the population\nabundance of individual clones under specific experimental\nperturbations. barbieQ supports barcode count data\npreprocessing, statistical testing, and visualization.",
  "Authors@R": "c(person(given = \"Liyang\",\nfamily = \"Fei\",\nrole = c(\"aut\", \"cre\"),\nemail = \"liyang.fei@petermac.org\",\ncomment = c(ORCID = \"0000-0002-3293-2094\"))\n)",
  "License": "GPL-3",
  "LazyData": "FALSE",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "biocViews": "Sequencing, Software, Regression, Preprocessing,\nVisualization",
  "BugReports": "https://github.com/Oshlack/barbieQ",
  "URL": "https://github.com/Oshlack/barbieQ/issues",
  "RoxygenNote": "7.3.2",
  "Config/testthat/edition": "3",
  "Roxygen": "list(markdown = TRUE)",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibxml2-dev perl libx11-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:04:55 UTC",
  "RemoteUrl": "https://github.com/bioc/barbieQ",
  "RemoteRef": "HEAD",
  "RemoteSha": "820164d3aa7917a8d225468d0782afe234990257",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 08:39:37 UTC",
    "User": "root"
  },
  "Author": "Liyang Fei [aut, cre] (ORCID: <https://orcid.org/0000-0002-3293-2094>)",
  "Maintainer": "Liyang Fei <liyang.fei@petermac.org>",
  "MD5sum": "2ba8777a42e2ff227b2af1a7c9ba0403",
  "_user": "bioc",
  "_type": "src",
  "_file": "barbieQ_1.5.0.tar.gz",
  "_fileid": "134cfb59a790c3b14542c4e44cc57f3b74c8100227a4c837aace7ca0da8478f3",
  "_filesize": 4338101,
  "_sha256": "134cfb59a790c3b14542c4e44cc57f3b74c8100227a4c837aace7ca0da8478f3",
  "_created": "2026-05-29T08:39:37.000Z",
  "_published": "2026-05-29T10:38:22.099Z",
  "_jobs": [
    {
      "job": 78467291101,
      "time": 214,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7286698573"
    },
    {
      "job": 78467291113,
      "time": 357,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7286740699"
    },
    {
      "job": 78467291091,
      "time": 355,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7286740123"
    },
    {
      "job": 78467291097,
      "time": 419,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7288739049"
    },
    {
      "job": 78467291108,
      "time": 275,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7288694882"
    },
    {
      "job": 78466124467,
      "time": 483,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286633729"
    },
    {
      "job": 78467291081,
      "time": 143,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286677259"
    },
    {
      "job": 78467291106,
      "time": 616,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7286818356"
    },
    {
      "job": 78467291115,
      "time": 847,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7286890435"
    },
    {
      "job": 78467291095,
      "time": 586,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7286810096"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 6
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26626990919",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/barbieQ",
  "_commit": {
    "id": "820164d3aa7917a8d225468d0782afe234990257",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381495
  },
  "_maintainer": {
    "name": "Liyang Fei",
    "email": "liyang.fei@petermac.org",
    "orcid": "0000-0002-3293-2094"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5",
      "role": "Depends"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "circlize",
      "role": "Imports"
    },
    {
      "package": "ComplexHeatmap",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "logistf",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.5.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.4.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "sequencing",
    "software",
    "regression",
    "preprocessing",
    "visualization"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "feiliyang",
      "count": 38,
      "uuid": 125324338
    },
    {
      "user": "jwokaty",
      "count": 2,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 255,
    "source": "https://www.bioconductor.org/packages/stats/bioc/barbieQ"
  },
  "_devurl": "https://github.com/oshlack/barbieq",
  "_searchresults": 4,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/barbieQ.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/oshlack/barbieq",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "clusterCorrelatingBarcodes",
    "createBarbieQ",
    "plotBarcodeHeatmap",
    "plotBarcodeMA",
    "plotBarcodePairCorrelation",
    "plotBarcodePareto",
    "plotBarcodeProportion",
    "plotBarcodePValue",
    "plotBarcodeSankey",
    "plotSamplePairCorrelation",
    "plotSignifBarcodeHeatmap",
    "plotSignifBarcodeProportion",
    "tagTopBarcodes",
    "testBarcodeSignif"
  ],
  "_datasets": [
    {
      "name": "monkeyHSPC",
      "title": "Monkey HSPC Cell Barcoding Data",
      "object": "monkeyHSPC",
      "file": "monkeyHSPC.rda",
      "class": [
        "SummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "clusterCorrelatingBarcodes",
      "title": "Cluster correlated Barcodes based on pairwise correlation",
      "topics": [
        "clusterCorrelatingBarcodes"
      ]
    },
    {
      "page": "createBarbieQ",
      "title": "Extract Barcode count data and build into a 'barbieQ' object for subsequent analysis",
      "topics": [
        "createBarbieQ"
      ]
    },
    {
      "page": "monkeyHSPC",
      "title": "Monkey HSPC Cell Barcoding Data",
      "topics": [
        "monkeyHSPC"
      ]
    },
    {
      "page": "plotBarcodeHeatmap",
      "title": "Plot Barcode CPM (or occurrence) across samples in a Heatmap",
      "topics": [
        "plotBarcodeHeatmap"
      ]
    },
    {
      "page": "plotBarcodeMA",
      "title": "Plot Barcodes catogorized by significant change using a dot plot",
      "topics": [
        "plotBarcodeMA"
      ]
    },
    {
      "page": "plotBarcodePairCorrelation",
      "title": "Plot Barcode pairwise correlation",
      "topics": [
        "plotBarcodePairCorrelation"
      ]
    },
    {
      "page": "plotBarcodePareto",
      "title": "Plot contributions of Barcodes split by _top_ v.s. _bottom_ in a circular bar plot.",
      "topics": [
        "plotBarcodePareto"
      ]
    },
    {
      "page": "plotBarcodeProportion",
      "title": "Plot Barcode contributions as mean Barcode proportion across samples",
      "topics": [
        "plotBarcodeProportion"
      ]
    },
    {
      "page": "plotBarcodePValue",
      "title": "Plot Barcodes categorized by significant change using a dot plot",
      "topics": [
        "plotBarcodePValue"
      ]
    },
    {
      "page": "plotBarcodeSankey",
      "title": "Plot total contributions of Barcodes grouped by _top_ vs. _bottom_ in a stacked bar plot.",
      "topics": [
        "plotBarcodeSankey"
      ]
    },
    {
      "page": "plotSamplePairCorrelation",
      "title": "Plot sample pairwise correlation in a Heatmap",
      "topics": [
        "plotSamplePairCorrelation"
      ]
    },
    {
      "page": "plotSignifBarcodeHeatmap",
      "title": "Plot Barcodes categorized by significant change using a Heatmap",
      "topics": [
        "plotSignifBarcodeHeatmap"
      ]
    },
    {
      "page": "plotSignifBarcodeProportion",
      "title": "Plot Barcode contributions as mean Barcode proportion across samples",
      "topics": [
        "plotSignifBarcodeProportion"
      ]
    },
    {
      "page": "tagTopBarcodes",
      "title": "Tag each Barcode as being part of the major contributors or not",
      "topics": [
        "tagTopBarcodes"
      ]
    },
    {
      "page": "testBarcodeSignif",
      "title": "Test significant change in Barcode proportion or occurrence between sample groups",
      "topics": [
        "testBarcodeSignif"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/barbieQ/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "Biobase",
    "BiocGenerics",
    "bit",
    "bit64",
    "boot",
    "broom",
    "circlize",
    "cli",
    "clipr",
    "clue",
    "cluster",
    "codetools",
    "colorspace",
    "ComplexHeatmap",
    "cpp11",
    "crayon",
    "data.table",
    "DelayedArray",
    "digest",
    "doParallel",
    "dplyr",
    "farver",
    "forcats",
    "foreach",
    "formula.tools",
    "generics",
    "GenomicRanges",
    "GetoptLong",
    "ggplot2",
    "glmnet",
    "GlobalOptions",
    "glue",
    "gtable",
    "haven",
    "hms",
    "igraph",
    "IRanges",
    "isoband",
    "iterators",
    "jomo",
    "labeling",
    "lattice",
    "lifecycle",
    "limma",
    "lme4",
    "logistf",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mgcv",
    "mice",
    "minqa",
    "mitml",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "operator.tools",
    "ordinal",
    "pan",
    "pillar",
    "pkgconfig",
    "png",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "Rdpack",
    "readr",
    "reformulas",
    "rjson",
    "rlang",
    "rpart",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "shape",
    "SparseArray",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "ucminf",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "barbieQ.Rmd",
      "filename": "barbieQ.html",
      "title": "barbieQ: An R package for analysing barcode count data from clonal tracking experiments",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Intallation",
        "Load Dependecy",
        "Load Package Data",
        "Example",
        "Create barbieQ Object",
        "Subset Dataset",
        "Tag Top Contributing Barcodes",
        "Visualize Sample Correlation",
        "Interaction with other tools",
        "Test Barcodes and Identify Significant Changes",
        "Differential Proportion",
        "Differential Occurrence",
        "References",
        "SessionInfo"
      ],
      "created": "2024-11-29 06:14:44",
      "modified": "2025-04-24 04:35:17",
      "commits": 14
    }
  ],
  "_score": 4,
  "_indexed": true,
  "_nocasepkg": "barbieq",
  "_universes": [
    "bioc",
    "oshlack"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.5.0",
      "date": "2026-05-29T08:43:32.000Z",
      "distro": "noble",
      "commit": "820164d3aa7917a8d225468d0782afe234990257",
      "fileid": "939e3654613e0f8b6596cc94f76564fbaf5614553c5caa5fcc8640090cd65cf8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626990919"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.5.0",
      "date": "2026-05-29T08:43:28.000Z",
      "distro": "noble",
      "commit": "820164d3aa7917a8d225468d0782afe234990257",
      "fileid": "e3f4da6badfe0afdc4ccdc6e81c55827eb09c2b322b647c9ce774ea1f2803434",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626990919"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.5.0",
      "date": "2026-05-29T10:34:56.000Z",
      "commit": "820164d3aa7917a8d225468d0782afe234990257",
      "fileid": "a5dfb42920ef0a425f8e568cd53058ec135cc9991ee8d8e74db5ee6919b9a8c1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626990919"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.5.0",
      "date": "2026-05-29T10:33:38.000Z",
      "commit": "820164d3aa7917a8d225468d0782afe234990257",
      "fileid": "545adb5424ccc76f4daa11e1f525b8d3d31bd28011a3c4529dc81b4f723d9ee7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626990919"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.5.0",
      "date": "2026-05-29T08:42:41.000Z",
      "commit": "820164d3aa7917a8d225468d0782afe234990257",
      "fileid": "79d80e7f2213a3a04542fa7b1c8bba020dc3a36ffd36459ff8cf9d5cc7f316a8",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626990919"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.5.0",
      "date": "2026-05-29T08:47:13.000Z",
      "commit": "820164d3aa7917a8d225468d0782afe234990257",
      "fileid": "1f25a1cd0987eab33427a1f40c2c496e5b15be7350a0c318ba3dfa6798ea3ca8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626990919"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.5.0",
      "date": "2026-05-29T08:51:28.000Z",
      "commit": "820164d3aa7917a8d225468d0782afe234990257",
      "fileid": "967ebb16e66aa86dd5e705ede4518295b0ba721b092ab3939e072c95d5261768",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626990919"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.5.0",
      "date": "2026-05-29T08:46:59.000Z",
      "commit": "820164d3aa7917a8d225468d0782afe234990257",
      "fileid": "379f4f7f6fb21998cb3f680e89a5dc6e183caae9ada219d09adeed6fecc1b8a1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626990919"
    }
  ]
}