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  "Title": "Automated analysis of high-throughput qPCR data",
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  "Author": "Heidi Dvinge, Paul Bertone",
  "Maintainer": "Matthew N. McCall <mccallm@gmail.com>",
  "Description": "Analysis of Ct values from high throughput quantitative\nreal-time PCR (qPCR) assays across multiple conditions or\nreplicates. The input data can be from spatially-defined\nformats such ABI TaqMan Low Density Arrays or OpenArray;\nLightCycler from Roche Applied Science; the CFX plates from\nBio-Rad Laboratories; conventional 96- or 384-well plates; or\nmicrofluidic devices such as the Dynamic Arrays from Fluidigm\nCorporation. HTqPCR handles data loading, quality assessment,\nnormalization, visualization and parametric or non-parametric\ntesting for statistical significance in Ct values between\nfeatures (e.g. genes, microRNAs).",
  "Reference": "Heidi Dvinge and Paul Bertone (2009). HTqPCR:\nHigh-throughput analysis and visualization of quantitative\nreal-time PCR data in R Bioinformatics.",
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    "featureNames",
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    "heatmapSig",
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    "n.samples",
    "n.wells",
    "normalizeCtData",
    "plotCtArray",
    "plotCtBoxes",
    "plotCtCard",
    "plotCtCategory",
    "plotCtCor",
    "plotCtDensity",
    "plotCtHeatmap",
    "plotCtHistogram",
    "plotCtLines",
    "plotCtOverview",
    "plotCtPairs",
    "plotCtPCA",
    "plotCtReps",
    "plotCtRQ",
    "plotCtScatter",
    "plotCtSignificance",
    "plotCtVariation",
    "plotCVBoxes",
    "readCtData",
    "sampleNames",
    "sampleNames<-",
    "setCategory",
    "setCt<-",
    "setCtHistory<-",
    "show",
    "summary",
    "ttestCtData"
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      "title": "Example processed qPCR data",
      "object": "qPCRpros",
      "file": "qPCRpros.RData",
      "class": [
        "qPCRset"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "qPCRraw",
      "title": "Example raw qPCR data.",
      "object": "qPCRraw",
      "file": "qPCRraw.RData",
      "class": [
        "qPCRset"
      ],
      "fields": [],
      "table": false,
      "tojson": false
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    {
      "page": "HTqPCR-package",
      "title": "Analysis of High-Throughput qPCR data (HTqPCR)",
      "topics": [
        "HTqPCR-package",
        "HTqPCR"
      ]
    },
    {
      "page": "cbind",
      "title": "Combine qPCRset objects",
      "topics": [
        "cbind",
        "cbind.qPCRset",
        "rbind",
        "rbind.qPCRset"
      ]
    },
    {
      "page": "changeCtLayout",
      "title": "Changing the dimensions (rows x columns) of qPCRset objects",
      "topics": [
        "changeCtLayout"
      ]
    },
    {
      "page": "clusterCt",
      "title": "Clustering of qPCR Ct values",
      "topics": [
        "clusterCt"
      ]
    },
    {
      "page": "filterCategory",
      "title": "Filter Ct values based on their feature categories.",
      "topics": [
        "filterCategory"
      ]
    },
    {
      "page": "filterCtData",
      "title": "Filter out features (genes) from qPCR data.",
      "topics": [
        "filterCtData"
      ]
    },
    {
      "page": "heatmapSig",
      "title": "Heatmap of deltadeltaCt values from qPCR data.",
      "topics": [
        "heatmapSig"
      ]
    },
    {
      "page": "limmaCtData",
      "title": "Differentially expressed features with qPCR: limma",
      "topics": [
        "limmaCtData"
      ]
    },
    {
      "page": "mannwhitneyCtData",
      "title": "Differentially expressed features with qPCR: Mann-Whitney",
      "topics": [
        "mannwhitneyCtData"
      ]
    },
    {
      "page": "normalizeCtData",
      "title": "Normalization of Ct values from qPCR data.",
      "topics": [
        "normalizeCtData"
      ]
    },
    {
      "page": "plotCtArray",
      "title": "Image plot of qPCR Ct values from an array format",
      "topics": [
        "plotCtArray"
      ]
    },
    {
      "page": "plotCtBoxes",
      "title": "Boxplots for qPCR Ct values.",
      "topics": [
        "plotCtBoxes"
      ]
    },
    {
      "page": "plotCtCard",
      "title": "Image plot of qPCR Ct values from a card format",
      "topics": [
        "plotCtCard"
      ]
    },
    {
      "page": "plotCtCategory",
      "title": "Summarising the feature categories for Ct values.",
      "topics": [
        "plotCtCategory"
      ]
    },
    {
      "page": "plotCtCor",
      "title": "Correlation between Ct values from qPCR data",
      "topics": [
        "plotCtCor"
      ]
    },
    {
      "page": "plotCtDensity",
      "title": "Distribution plot for qPCR Ct values.",
      "topics": [
        "plotCtDensity"
      ]
    },
    {
      "page": "plotCtHeatmap",
      "title": "Heatmap of qPCR Ct values.",
      "topics": [
        "plotCtHeatmap"
      ]
    },
    {
      "page": "plotCtHistogram",
      "title": "Histrogram of Ct values from qPCR experiments.",
      "topics": [
        "plotCtHistogram"
      ]
    },
    {
      "page": "plotGenes",
      "title": "Plotting Ct values from qPCR across multiple samples.",
      "topics": [
        "plotCtLines"
      ]
    },
    {
      "page": "plotCtOverview",
      "title": "Overview plot of qPCR Ct values across multiple conditions.",
      "topics": [
        "plotCtOverview"
      ]
    },
    {
      "page": "plotCtPairs",
      "title": "Pairwise scatterplot of multiple sets of Ct values from qPCR data.",
      "topics": [
        "plotCtPairs"
      ]
    },
    {
      "page": "plotCtPCA",
      "title": "PCA for qPCR Ct values.",
      "topics": [
        "plotCtPCA"
      ]
    },
    {
      "page": "plotCtReps",
      "title": "Scatter plot of features analysed twice during each qPCR experiment.",
      "topics": [
        "plotCtReps"
      ]
    },
    {
      "page": "plotCtRQ",
      "title": "Plot the relative quantification of Ct values from qPCR experiments.",
      "topics": [
        "plotCtRQ"
      ]
    },
    {
      "page": "plotCtScatter",
      "title": "Scatterplot of two sets of Ct values from qPCR data.",
      "topics": [
        "plotCtScatter"
      ]
    },
    {
      "page": "plotCtSignificance",
      "title": "Barplot with Ct values between genes from qPCR.",
      "topics": [
        "plotCtSignificance"
      ]
    },
    {
      "page": "plotCtVariation",
      "title": "Plot variation in Ct values across replicates",
      "topics": [
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      ]
    },
    {
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      "title": "Boxplots of CV for qPCR Ct values.",
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      ]
    },
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      "title": "Example processed qPCR data",
      "topics": [
        "qPCRpros"
      ]
    },
    {
      "page": "qPCRraw",
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      "topics": [
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        "featureCategory",
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        ".readCtCFX",
        ".readCtLightCycler",
        ".readCtOpenArray",
        ".readCtPlain",
        ".readCtSDS",
        "readCtData"
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    },
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      "page": "setCategory",
      "title": "Assign categories to Ct values from qPCR data.",
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      ]
    },
    {
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