{
  "_id": "6a2a9a567b7a29ca60050da4",
  "Package": "VDJdive",
  "Title": "Analysis Tools for 10X V(D)J Data",
  "Version": "1.15.1",
  "Authors@R": "c(\nperson(\"Kelly\", \"Street\", role = c(\"aut\", \"cre\"), email = \"street.kelly@gmail.com\", comment = c(ORCID = \"0000-0001-6379-5013\")),\nperson(\"Mercedeh\", \"Movassagh\", role = \"aut\", email = \"mercedeh@ds.dfci.harvard.edu\", comment = c(ORCID = \"0000-0001-7690-0230\")),\nperson(\"Jill\", \"Lundell\", role = \"aut\", email = \"jflundell@gmail.com\", comment = c(ORCID = \"0000-0002-6048-4700\")),\nperson(\"Jared\", \"Brown\", role = \"ctb\"),\nperson(\"Linglin\", \"Huang\", role = \"ctb\"),\nperson(\"Mingzhi\", \"Ye\", role = \"ctb\"))",
  "Description": "This package provides functions for handling and analyzing\nimmune receptor repertoire data, such as produced by the\nCellRanger V(D)J pipeline. This includes reading the data into\nR, merging it with paired single-cell data, quantifying\nclonotype abundances, calculating diversity metrics, and\nproducing common plots. It implements the E-M Algorithm for\nclonotype assignment, along with other methods, which makes use\nof ambiguous cells for improved quantification.",
  "License": "Artistic-2.0",
  "URL": "https://github.com/kstreet13/VDJdive",
  "BugReports": "https://github.com/kstreet13/VDJdive/issues",
  "biocViews": "Software, ImmunoOncology, SingleCell, Annotation, RNASeq,\nTargetedResequencing",
  "Encoding": "UTF-8",
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  "Collate": "'RcppExports.R' 'clonoStats_class.R' 'abundanceVDJ.R'\n'barVDJ.R' 'boxVDJ.R' 'calculateDiversity.R'\n'clonoStats_helpers.R' 'clonoStats.R' 'contigs.R' 'pieVDJ.R'\n'runBreakaway.R' 'runVDJPCA.R' 'scatterVDJ.R' 'setup.R'\n'utils.R'",
  "Config/Bioconductor/UnsupportedPlatforms": "windows",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-29 18:37:27 UTC",
  "RemoteUrl": "https://github.com/bioc/VDJdive",
  "RemoteRef": "HEAD",
  "RemoteSha": "e6b1f6bd749238aaec49033f84304d66c13eca6a",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-11 11:12:21 UTC",
    "User": "root"
  },
  "Author": "Kelly Street [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-6379-5013>),\nMercedeh Movassagh [aut] (ORCID:\n<https://orcid.org/0000-0001-7690-0230>),\nJill Lundell [aut] (ORCID: <https://orcid.org/0000-0002-6048-4700>),\nJared Brown [ctb],\nLinglin Huang [ctb],\nMingzhi Ye [ctb]",
  "Maintainer": "Kelly Street <street.kelly@gmail.com>",
  "MD5sum": "fe97a7ad2b5231d8bc46b31289027722",
  "_user": "bioc",
  "_type": "src",
  "_file": "VDJdive_1.15.1.tar.gz",
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  "_filesize": 486768,
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  "_created": "2026-06-11T11:12:21.000Z",
  "_published": "2026-06-11T11:21:58.169Z",
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    "author": "A Wokaty <awokaty@users.noreply.github.com>",
    "committer": "A Wokaty <awokaty@users.noreply.github.com>",
    "message": "Bump version\n",
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    "email": "street.kelly@gmail.com",
    "login": "kstreet13",
    "description": "Assistant Professor of Population and Public Health Sciences, Division of Biostatistics",
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    "orcid": "0000-0001-6379-5013"
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  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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  "_contributors": [
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    "source": "https://www.bioconductor.org/packages/stats/bioc/VDJdive"
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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  "_homeurl": "https://github.com/kstreet13/vdjdive",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "abundanceVDJ",
    "addVDJtoSCE",
    "barVDJ",
    "boxVDJ",
    "calculateDiversity",
    "clonoAbundance",
    "clonoAssignment",
    "clonoFrequency",
    "clonoGroup",
    "clonoNames",
    "clonoStats",
    "pieVDJ",
    "readVDJcontigs",
    "runBreakaway",
    "runVDJPCA",
    "scatterVDJ",
    "show",
    "splitClonotypes",
    "summarizeClonotypes",
    "writeVDJcontigs"
  ],
  "_datasets": [
    {
      "name": "contigs",
      "title": "SplitDataFrameList containing AIRR-seq (TCR) data for six cells",
      "object": "contigs",
      "file": "contigs.rda",
      "class": [
        "CompressedSplitDFrameList"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
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  "_help": [
    {
      "page": "abundanceVDJ",
      "title": "Create an abundance graph for clonotype expansion",
      "topics": [
        "abundanceVDJ",
        "abundanceVDJ,clonoStats-method"
      ]
    },
    {
      "page": "addVDJtoSCE",
      "title": "Add 10X CellRanger V(D)J data to SingleCellExperiment",
      "topics": [
        "addVDJtoSCE",
        "addVDJtoSCE,character,SingleCellExperiment-method",
        "addVDJtoSCE,SplitDataFrameList,SingleCellExperiment-method"
      ]
    },
    {
      "page": "barVDJ",
      "title": "Create a bar graph for clonotype expansion",
      "topics": [
        "barVDJ",
        "barVDJ,clonoStats-method",
        "barVDJ,Matrix-method",
        "barVDJ,matrix-method"
      ]
    },
    {
      "page": "boxVDJ",
      "title": "Create a box plot for diversity measures",
      "topics": [
        "boxVDJ",
        "boxVDJ,matrix-method"
      ]
    },
    {
      "page": "calculateDiversity",
      "title": "Sample diversity estimation",
      "topics": [
        "calculateDiversity",
        "calculateDiversity,clonoStats-method",
        "calculateDiversity,SingleCellExperiment-method"
      ]
    },
    {
      "page": "clonoStats",
      "title": "Assign cell-level clonotypes and calculate abundances",
      "topics": [
        "clonoStats",
        "clonoStats,clonoStats-method",
        "clonoStats,SingleCellExperiment-method",
        "clonoStats,SplitDataFrameList-method"
      ]
    },
    {
      "page": "clonoStats-class",
      "title": "'clonoStats' object class",
      "topics": [
        "clonoAbundance",
        "clonoAbundance,clonoStats-method",
        "clonoAbundance,SingleCellExperiment-method",
        "clonoAssignment",
        "clonoAssignment,clonoStats-method",
        "clonoAssignment,SingleCellExperiment-method",
        "clonoFrequency",
        "clonoFrequency,clonoStats-method",
        "clonoFrequency,SingleCellExperiment-method",
        "clonoGroup",
        "clonoGroup,clonoStats-method",
        "clonoGroup,SingleCellExperiment-method",
        "clonoNames",
        "clonoNames,clonoStats-method",
        "clonoNames,SingleCellExperiment-method",
        "clonoStats-class",
        "show,clonoStats-method"
      ]
    },
    {
      "page": "contigs",
      "title": "SplitDataFrameList containing AIRR-seq (TCR) data for six cells",
      "topics": [
        "contigs"
      ]
    },
    {
      "page": "pieVDJ",
      "title": "Create a pie chart for clonotype expansion",
      "topics": [
        "pieVDJ",
        "pieVDJ,clonoStats-method",
        "pieVDJ,Matrix-method",
        "pieVDJ,matrix-method"
      ]
    },
    {
      "page": "readVDJcontigs",
      "title": "Load 10X CellRanger V(D)J data",
      "topics": [
        "readVDJcontigs",
        "readVDJcontigs,character-method"
      ]
    },
    {
      "page": "runBreakaway",
      "title": "Clonotype richness estimation with Breakaway",
      "topics": [
        "runBreakaway",
        "runBreakaway,clonoStats-method"
      ]
    },
    {
      "page": "runVDJPCA",
      "title": "Run PCA on clonotype abundance matrix",
      "topics": [
        "runVDJPCA",
        "runVDJPCA,clonoStats-method"
      ]
    },
    {
      "page": "scatterVDJ",
      "title": "Create a scatterplot for diversity evenness and abundance",
      "topics": [
        "scatterVDJ",
        "scatterVDJ,matrix-method"
      ]
    },
    {
      "page": "splitClonotypes",
      "title": "Split cell-level clonotype counts by sample",
      "topics": [
        "splitClonotypes",
        "splitClonotypes,clonoStats-method",
        "splitClonotypes,Matrix-method",
        "splitClonotypes,matrix-method",
        "splitClonotypes,SingleCellExperiment-method"
      ]
    },
    {
      "page": "summarizeClonotypes",
      "title": "Get sample-level clonotype counts",
      "topics": [
        "summarizeClonotypes",
        "summarizeClonotypes,clonoStats-method",
        "summarizeClonotypes,Matrix-method",
        "summarizeClonotypes,matrix-method",
        "summarizeClonotypes,SingleCellExperiment-method"
      ]
    },
    {
      "page": "writeVDJcontigs",
      "title": "Write V(D)J contig data in 10X format",
      "topics": [
        "writeVDJcontigs",
        "writeVDJcontigs,character,SplitDataFrameList-method"
      ]
    }
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      "title": "VDJdive Workflow",
      "author": "Kelly Street, Mercedeh Movassagh, Jill Lundell",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Read in 10X data",
        "Merging V(D)J and scRNAseq Data",
        "Assign Clonotypes and Calculate Summaries",
        "Diversity",
        "Cluster Diversity",
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