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  "Title": "Immunoglobulin Clonal Lineage and Diversity Analysis",
  "Description": "Provides methods for high-throughput adaptive immune\nreceptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In\nparticular, immunoglobulin (Ig) sequence lineage\nreconstruction, lineage topology analysis, diversity profiling,\namino acid property analysis and gene usage. Citations: Gupta\nand Vander Heiden, et al (2017)\n<doi:10.1093/bioinformatics/btv359>, Stern, Yaari and Vander\nHeiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.",
  "License": "AGPL-3",
  "URL": "https://alakazam.readthedocs.io/",
  "BugReports": "https://github.com/immcantation/alakazam/issues",
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  "Repository": "https://immcantation.r-universe.dev",
  "Date/Publication": "2026-05-01 07:53:08 UTC",
  "RemoteUrl": "https://github.com/immcantation/alakazam",
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  "Packaged": {
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    "User": "root"
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  "Author": "Susanna Marquez [cre, aut],\nNamita Gupta [aut],\nNima Nouri [aut],\nRuoyi Jiang [aut],\nJulian Zhou [aut],\nKenneth Hoehn [aut],\nDaniel Gadala-Maria [ctb],\nEdel Aron [ctb],\nCole Jensen [aut],\nGisela Gabernet [ctb],\nCaroline Sullivan [ctb],\nHailong Meng [ctb],\nHuimin Lyu [ctb],\nBurhan Sabuwala [ctb],\nJason Vander Heiden [aut],\nSteven Kleinstein [aut, cph]",
  "Maintainer": "Susanna Marquez <susanna.marquez@yale.edu>",
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    "maskSeqGaps",
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    "padSeqEnds",
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    "summarizeSubtrees",
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    "testDiversity",
    "testEdges",
    "testMRCA",
    "TR_COLORS",
    "translateDNA",
    "translateStrings",
    "writeChangeoDb"
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      "name": "Example10x",
      "title": "",
      "object": "Example10x",
      "class": [
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        "tbl",
        "data.frame"
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        "sequence",
        "rev_comp",
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        "fwr1",
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        "umi_count",
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        "d_call_10x",
        "j_call_10x",
        "junction_10x",
        "junction_10x_aa"
      ],
      "rows": 194,
      "table": true,
      "tojson": true
    },
    {
      "name": "ExampleDb",
      "title": "",
      "object": "ExampleDb",
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        "tbl",
        "data.frame"
      ],
      "fields": [
        "sequence_id",
        "sequence_alignment",
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        "np1_length",
        "np2_length",
        "duplicate_count",
        "clone_id",
        "sample_id",
        "locus"
      ],
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      "table": true,
      "tojson": true
    },
    {
      "name": "ExampleDbChangeo",
      "title": "",
      "object": "ExampleDbChangeo",
      "class": [
        "tbl_df",
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        "data.frame"
      ],
      "fields": [
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        "SEQUENCE_IMGT",
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        "DUPCOUNT",
        "CLONE"
      ],
      "rows": 1999,
      "table": true,
      "tojson": true
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    {
      "name": "ExampleTrees",
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      "object": "ExampleTrees",
      "class": [
        "list"
      ],
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