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  "Authors@R": "c(person(\"Mohamed\", \"Uduman\", role=c(\"aut\"), \nemail=\"mohamed.uduman@yale.edu\"),\nperson(\"Namita\", \"Gupta\", role=c(\"aut\"),\nemail=\"namita.gupta@yale.edu\"),\nperson(\"Susanna\", \"Marquez\", role=c(\"aut\",\"cre\"),\nemail=\"susanna.marquez@yale.edu\"),\nperson(\"Julian\", \"Zhou\", role=c(\"aut\"),\nemail=\"julian.zhou@yale.edu\"),\nperson(\"Nima\", \"Nouri\", role=c(\"aut\"),\nemail=\"nima.nouri@yale.edu\"),\nperson(\"Noah\", \"Yann Lee\", role=c(\"aut\"),\nemail=\"noah.yann.lee@yale.edu\"),\nperson(\"Ang\", \"Cui\", role=c(\"ctb\"),\nemail=\"angcui@mit.edu\"),\nperson(\"Jason\", \"Vander Heiden\", role=c(\"aut\"),\nemail=\"jason.vanderheiden@gmail.com\"),\nperson(\"Gur\", \"Yaari\", role=c(\"aut\"),\nemail=\"gur.yaari@biu.ac.il\"),\nperson(\"Steven\", \"Kleinstein\", role=c(\"aut\", \"cph\"),\nemail=\"steven.kleinstein@yale.edu\"))",
  "Title": "Immunoglobulin Somatic Hypermutation Analysis",
  "Description": "Provides a computational framework for analyzing mutations\nin immunoglobulin (Ig) sequences. Includes methods for Bayesian\nestimation of antigen-driven selection pressure, mutational\nload quantification, building of somatic hypermutation (SHM)\nmodels, and model-dependent distance calculations. Also\nincludes empirically derived models of SHM for both mice and\nhumans. Citations: Gupta and Vander Heiden, et al (2015)\n<doi:10.1093/bioinformatics/btv359>, Yaari, et al (2012)\n<doi:10.1093/nar/gks457>, Yaari, et al (2013)\n<doi:10.3389/fimmu.2013.00358>, Cui, et al (2016)\n<doi:10.4049/jimmunol.1502263>.",
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    "calcBaseline",
    "calcExpectedMutations",
    "calcObservedMutations",
    "calcTargetingDistance",
    "calculateMutability",
    "collapseClones",
    "consensusSequence",
    "convertNumbering",
    "createBaseline",
    "createMutabilityMatrix",
    "createMutationDefinition",
    "createRegionDefinition",
    "createSubstitutionMatrix",
    "createTargetingMatrix",
    "createTargetingModel",
    "distToNearest",
    "editBaseline",
    "expectedMutations",
    "extendMutabilityMatrix",
    "extendSubstitutionMatrix",
    "findThreshold",
    "groupBaseline",
    "makeAverage1merMut",
    "makeAverage1merSub",
    "makeDegenerate5merMut",
    "makeDegenerate5merSub",
    "makeGraphDf",
    "minNumMutationsTune",
    "minNumSeqMutationsTune",
    "observedMutations",
    "plot",
    "plotBaselineDensity",
    "plotBaselineSummary",
    "plotDensityThreshold",
    "plotGmmThreshold",
    "plotMutability",
    "plotSlideWindowTune",
    "plotTune",
    "print",
    "setRegionBoundaries",
    "shmulateSeq",
    "shmulateTree",
    "slideWindowDb",
    "slideWindowSeq",
    "slideWindowTune",
    "slideWindowTunePlot",
    "summarizeBaseline",
    "summary",
    "testBaseline",
    "writeTargetingDistance"
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      "title": "",
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      "table": false,
      "tojson": false
    },
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      "title": "",
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        "array"
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        "C",
        "G",
        "T"
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      "table": true,
      "tojson": true
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    },
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      "tojson": false
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