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  "Description": "Analysis of DNA copy number in single cells using custom\ngenome-wide targeted DNA sequencing panels for the Mission Bio\nTapestri platform. Users can easily parse, manipulate, and\nvisualize datasets produced from the automated 'Tapestri\nPipeline', with support for normalization, clustering, and copy\nnumber calling. Functions are also available to deconvolute\nmultiplexed samples by genotype and parsing barcoded reads from\nexogenous lentiviral constructs.",
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    "grnaProbe<-",
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    "runPCA",
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      ]
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    {
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      ]
    },
    {
      "page": "calcCopyNumber",
      "title": "Calculate relative copy number value for each cell-probe unit using reference sample",
      "concept": [
        "copy number"
      ],
      "topics": [
        "calcCopyNumber",
        "generateControlCopyNumberTemplate"
      ]
    },
    {
      "page": "calcGMMCopyNumber",
      "title": "Call copy number for each cell-chromosome using Gaussian mixture models",
      "concept": [
        "copy number"
      ],
      "topics": [
        "calcGMMCopyNumber"
      ]
    },
    {
      "page": "calcNormCounts",
      "title": "Normalize raw counts",
      "concept": [
        "copy number"
      ],
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      ]
    },
    {
      "page": "calcSmoothCopyNumber",
      "title": "Smooth copy number values across chromosomes and chromosome arms",
      "concept": [
        "copy number"
      ],
      "topics": [
        "calcSmoothCopyNumber"
      ]
    },
    {
      "page": "callSampleLables",
      "title": "Call sample labels based on feature counts",
      "concept": [
        "barcoded reads"
      ],
      "topics": [
        "callSampleLables"
      ]
    },
    {
      "page": "corner",
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      ]
    },
    {
      "page": "countBarcodedReads",
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      "concept": [
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      ],
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        "countBarcodedReadsFromContig"
      ]
    },
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      "page": "CreateTapestriExperiment",
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      "concept": [
        "build experiment"
      ],
      "topics": [
        "createTapestriExperiment"
      ]
    },
    {
      "page": "slotGettersSetters",
      "title": "Getter and Setter functions for 'TapestriExperiment' slots",
      "concept": [
        "build experiment"
      ],
      "topics": [
        "barcodeProbe",
        "barcodeProbe,TapestriExperiment-method",
        "barcodeProbe<-",
        "barcodeProbe<-,TapestriExperiment-method",
        "Custom Slot Getters and Setters",
        "gmmParams",
        "gmmParams,TapestriExperiment-method",
        "grnaProbe",
        "grnaProbe,TapestriExperiment-method",
        "grnaProbe<-",
        "grnaProbe<-,TapestriExperiment-method"
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    },
    {
      "page": "getChrOrder",
      "title": "Get chromosome order from a string of chromosome/contig names",
      "concept": [
        "build experiment"
      ],
      "topics": [
        "getChrOrder"
      ]
    },
    {
      "page": "getCytobands",
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      "concept": [
        "build experiment"
      ],
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      ]
    },
    {
      "page": "getGMMBoundaries",
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      "concept": [
        "copy number"
      ],
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      "page": "getTidyData",
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      "concept": [
        "copy number"
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      "version": "1.0.2",
      "date": "2026-10-01T09:25:35.000Z",
      "commit": "8922a7f37f6b512fb0c4a577adab517f2d80050b",
      "fileid": "https://r2.ropensci.org/b06e2240244992fbcd6514968f308542d180283dd79fa89959a0834b7dfd9bae",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/joeymays/actions/runs/36841832025"
    }
  ]
}