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  "Type": "Package",
  "Date": "2024-08-22",
  "Title": "Hierarchical Epitope pROtein biNding",
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  "Date/Publication": "2026-04-28 13:01:16 UTC",
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  "Author": "Sean McIlwain [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-3820-8400>),\nIrene Ong [aut] (ORCID: <https://orcid.org/0000-0002-9353-6941>)",
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    ".HERONSequenceDataSet",
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    "calcCombPValues",
    "calcEpitopePValues",
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    "calcProbePValuesWUnpaired",
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    "findEpitopeSegments",
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    "getEpitopeIDsToProbeIDs",
    "getEpitopeProbeIDs",
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    "getEpitopeStart",
    "getEpitopeStop",
    "getKofN",
    "getProteinLabel",
    "getProteinStart",
    "getProteinTiling",
    "HERONEpitopeDataSet",
    "HERONProbeDataSet",
    "HERONProteinDataSet",
    "HERONSequenceDataSet",
    "log2Transform",
    "makeEpitopeCalls",
    "makeProbeCalls",
    "makeProteinCalls",
    "min_max",
    "oneHitEpitopes",
    "oneHitProbes",
    "oneProbeEpitopes",
    "pvalue_to_zscore",
    "quantileNormalize",
    "smoothProbeDS"
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      "name": "heffron2021_wuhan",
      "title": "SARS CoV-2 Wuhan Peptide Binding Array Data",
      "object": "heffron2021_wuhan",
      "file": "heffron2021_wuhan.rda",
      "class": [
        "HERONSequenceDataSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
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  "_help": [
    {
      "page": "addSequenceAnnotations",
      "title": "Add Sequence Annotations for Epitopes",
      "topics": [
        "addSequenceAnnotations"
      ]
    },
    {
      "page": "calcCombPValues",
      "title": "Calculate p-values using the \"exprs\" assay",
      "topics": [
        "calcCombPValues"
      ]
    },
    {
      "page": "calcEpitopePValues",
      "title": "Calculate epitope-level p-values",
      "topics": [
        "calcEpitopePValues"
      ]
    },
    {
      "page": "calcProbePValuesTPaired",
      "title": "Calculate Probe p-values using a differential paired t-test",
      "topics": [
        "calcProbePValuesTPaired"
      ]
    },
    {
      "page": "calcProbePValuesTUnpaired",
      "title": "Calculate Probe p-values using a differential unpaired t-test",
      "topics": [
        "calcProbePValuesTUnpaired"
      ]
    },
    {
      "page": "calcProbePValuesWUnpaired",
      "title": "Calculate Probe p-values using a two-sample wilcoxon test",
      "topics": [
        "calcProbePValuesWUnpaired"
      ]
    },
    {
      "page": "calcProteinPValues",
      "title": "Calculate protein-level p-values",
      "topics": [
        "calcProteinPValues"
      ]
    },
    {
      "page": "catSequences",
      "title": "Concatenate sequences together based upon their start positions. Assumes the probe sequences have an overlap.",
      "topics": [
        "catSequences"
      ]
    },
    {
      "page": "convertSequenceDSToProbeDS",
      "title": "Convert HERONSequenceDataSet to HERONProbeDataSet",
      "topics": [
        "convertSequenceDSToProbeDS"
      ]
    },
    {
      "page": "findBlocksProbeT",
      "title": "Find Blocks of consecutive probes",
      "topics": [
        "findBlocksProbeT"
      ]
    },
    {
      "page": "findBlocksT",
      "title": "Find consecutive probes",
      "topics": [
        "findBlocksT"
      ]
    },
    {
      "page": "findEpitopeSegments",
      "title": "Find Epitopes from probe stats and calls.",
      "topics": [
        "findEpitopeSegments"
      ]
    },
    {
      "page": "getEpitopeID",
      "title": "Create EpitopeID from protein, first and last probes",
      "topics": [
        "getEpitopeID"
      ]
    },
    {
      "page": "getEpitopeIDsToProbeIDs",
      "title": "Get probe ids from a vector of epitope ids",
      "topics": [
        "getEpitopeIDsToProbeIDs"
      ]
    },
    {
      "page": "getEpitopeProbeIDs",
      "title": "Get the vector of probes from an epitope id",
      "topics": [
        "getEpitopeProbeIDs"
      ]
    },
    {
      "page": "getEpitopeProtein",
      "title": "Obtain Protein Id from Epitope ID",
      "topics": [
        "getEpitopeProtein"
      ]
    },
    {
      "page": "getEpitopeStart",
      "title": "Obtain first probe's protein start position from Epitope ID",
      "topics": [
        "getEpitopeStart"
      ]
    },
    {
      "page": "getEpitopeStop",
      "title": "Obtain last probe's protein start position from EpitopeID",
      "topics": [
        "getEpitopeStop"
      ]
    },
    {
      "page": "getKofN",
      "title": "Get K of N statistics from an experiment with padj and calls",
      "topics": [
        "getKofN"
      ]
    },
    {
      "page": "getProteinLabel",
      "title": "Get Protein Label from Probe",
      "topics": [
        "getProteinLabel"
      ]
    },
    {
      "page": "getProteinStart",
      "title": "Get the amino-acid starting position of the probe within the protein.",
      "topics": [
        "getProteinStart"
      ]
    },
    {
      "page": "getProteinTiling",
      "title": "Get Protein Tiling",
      "topics": [
        "getProteinTiling"
      ]
    },
    {
      "page": "heffron2021_wuhan",
      "title": "SARS CoV-2 Wuhan Peptide Binding Array Data",
      "topics": [
        "heffron2021_wuhan"
      ]
    },
    {
      "page": "HERONEpitopeDataSet",
      "title": "HERONEpitopeDataSet object and constructors",
      "topics": [
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        "HERONEpitopeDataSet",
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    {
      "page": "HERONProbeDataSet",
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        "HERONProbeDataSet-class"
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    {
      "page": "HERONProteinDataSet",
      "title": "HERONProteinDataSet object and constructors",
      "topics": [
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        "HERONProteinDataSet",
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        "HERONSequenceDataSet",
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      "page": "log2Transform",
      "title": "log2 transform the \"exprs\" assay",
      "topics": [
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    {
      "page": "makeEpitopeCalls",
      "title": "Make Epitope Calls",
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      "page": "makeProbeCalls",
      "title": "Making Probe-level Calls",
      "topics": [
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    {
      "page": "makeProteinCalls",
      "title": "Make Protein-level Calls",
      "topics": [
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      ]
    },
    {
      "page": "min_max",
      "title": "Cap vector at minimum/maximum values",
      "topics": [
        "min_max"
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    },
    {
      "page": "oneHitEpitopes",
      "title": "Find One-hit epitopes",
      "topics": [
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    },
    {
      "page": "oneHitProbes",
      "title": "Find one hit probes",
      "topics": [
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      ]
    },
    {
      "page": "oneProbeEpitopes",
      "title": "Indicate which epitopes are just one probe.",
      "topics": [
        "oneProbeEpitopes"
      ]
    },
    {
      "page": "probeHitSupported",
      "title": "Find probe hits with a consecutive probe or another sample",
      "topics": [
        "probeHitSupported"
      ]
    },
    {
      "page": "pvalue_to_zscore",
      "title": "Convert p-value matrix to a z-score matrix",
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    },
    {
      "page": "quantileNormalize",
      "title": "Normalize the exprs assay using quantile normalization",
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    },
    {
      "page": "smoothProbeDS",
      "title": "Smooth probes across protein tiling",
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      "title": "Analyzing High Density Peptide Array Data using HERON",
      "engine": "knitr::rmarkdown",
      "headings": [
        "HERON",
        "Installation",
        "Example",
        "The HERONSequenceData object",
        "Sequence matrix",
        "colData",
        "Probe metadata",
        "Creating the HERONSequenceData object",
        "Pre-process data",
        "Calculate probe-level p-values",
        "Obtain probe-level calls",
        "Find Epitope Segments using the unique method",
        "Calculate Epitope-level p-values",
        "Obtain Epitope-level calls",
        "Calculate Protein-level p-values",
        "Obtain Protein-level calls",
        "Other",
        "Find Epitope Segments using the hclust method",
        "binary calls with hamming distance",
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        "Find Epitope Segments using the skater method",
        "Other meta p-value methods",
        "Making z-score cutoff calls",
        "Smoothing across probes",
        "Calculate paired t-tests",
        "Use the wilcox test for probe-level p-values",
        "Use of the condition column",
        "Funding",
        "Acknowledgments",
        "Session Info"
      ],
      "created": "2022-10-11 14:29:47",
      "modified": "2024-08-22 20:09:24",
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