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    "example.table",
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    "fit.nb.glm.1u",
    "get.mean.hat",
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    "get.rel.mean",
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    "hist2d",
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    "plot.nb.dispersion",
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    "print.nb.dispersion",
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      "object": "arab",
      "file": "arab.rda",
      "class": [
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        "array"
      ],
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        "mock1",
        "mock2",
        "mock3",
        "hrcc1",
        "hrcc2",
        "hrcc3"
      ],
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      "table": true,
      "tojson": true
    }
  ],
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    {
      "page": "NBPSeq-package",
      "title": "Negative Binomial Regression Models for Statistical Analysis of RNA-Sequencing Data",
      "topics": [
        "NBPSeq-package",
        "NBPSeq"
      ]
    },
    {
      "page": "sub-.nb.data",
      "title": "hello",
      "topics": [
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      ]
    },
    {
      "page": "arab",
      "title": "Arabidopsis RNA-Seq Data Set",
      "topics": [
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      ]
    },
    {
      "page": "compute.tail.prob",
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      "topics": [
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      "topics": [
        "disp.by.group"
      ]
    },
    {
      "page": "disp.nbp",
      "title": "(private) Specify a NBP dispersion model",
      "topics": [
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    },
    {
      "page": "disp.nbq",
      "title": "(private) Specify a NBQ dispersion model",
      "topics": [
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      ]
    },
    {
      "page": "disp.nbs",
      "title": "(private) Specify a NBS dispersion model",
      "topics": [
        "disp.nbs"
      ]
    },
    {
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      "title": "Dispersion precitor",
      "topics": [
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      ]
    },
    {
      "page": "disp.step",
      "title": "(private) Specify a piecewise constant dispersion model",
      "topics": [
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      ]
    },
    {
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      "title": "(private) Specify a NB2, NBP, NBS, NBS, or STEP dispersion model",
      "topics": [
        "disp.fun.nb2",
        "disp.fun.nbp",
        "disp.fun.nbq",
        "disp.fun.nbs",
        "disp.fun.step",
        "Dispersion Models"
      ]
    },
    {
      "page": "estimate.disp",
      "title": "Fit a parametric disperison model to thinned counts",
      "topics": [
        "estimate.disp"
      ]
    },
    {
      "page": "estimate.dispersion",
      "title": "Estimate Negative Binomial Dispersion",
      "topics": [
        "estimate.dispersion"
      ]
    },
    {
      "page": "estimate.norm.factors",
      "title": "Estiamte Normalization Factors",
      "topics": [
        "estimate.norm.factors"
      ]
    },
    {
      "page": "exact.nb.test",
      "title": "Exact Negative Binomial Test for Differential Gene Expression",
      "topics": [
        "exact.nb.test"
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    },
    {
      "page": "filter.mu.pre",
      "title": "Create a logical vector specifyfing the subset of rows to be used when estimating the dispersion model",
      "topics": [
        "filter.mu.pre"
      ]
    },
    {
      "page": "fit.nb.glm.1",
      "title": "Fit a single negative binomial (NB) log-linear regression model with known dispersion paramreters",
      "topics": [
        "fit.nb.glm.1"
      ]
    },
    {
      "page": "fit.nb.glm.1u",
      "title": "Fit a single negative binomial (NB) log-linear regression model with a common unknown dispersion paramreter",
      "topics": [
        "fit.nb.glm.1u"
      ]
    },
    {
      "page": "get.mean.hat",
      "title": "(private) Extract row means of the pseudo counts for the specified group from an 'nbp' object.",
      "topics": [
        "get.mean.hat"
      ]
    },
    {
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      "title": "(private) Retrieve nbp parameters for one of the treatment groups from an nbp object",
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        "get.nbp.pars"
      ]
    },
    {
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      "topics": [
        "get.rel.mean"
      ]
    },
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      "topics": [
        "get.var.hat"
      ]
    },
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      "page": "hist2d",
      "title": "2-d Histogram",
      "topics": [
        "hist2d"
      ]
    },
    {
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      "title": "(private) One-dimensional HOA test for a regression coefficient in an NB GLM model",
      "topics": [
        "hoa.1d"
      ]
    },
    {
      "page": "hoa.hd",
      "title": "(private) HOA test for regression coefficients in an NBP GLM model",
      "topics": [
        "hoa.hd"
      ]
    },
    {
      "page": "irls.nb",
      "title": "(private) Estiamte the regression coefficients in an NB GLM model",
      "topics": [
        "irls.nb"
      ]
    },
    {
      "page": "irls.nb.1",
      "title": "Estimate the regression coefficients in an NB GLM model",
      "topics": [
        "irls.nb.1"
      ]
    },
    {
      "page": "l.nb",
      "title": "(private) The Log Likelihood of a NB Model",
      "topics": [
        "l.nb"
      ]
    },
    {
      "page": "log.phi.nb2",
      "title": "(private) A NBP dispersion model",
      "topics": [
        "log.phi.nb2"
      ]
    },
    {
      "page": "log.phi.nbp",
      "title": "(private) A NBP dispersion model",
      "topics": [
        "log.phi.nbp"
      ]
    },
    {
      "page": "log.phi.nbq",
      "title": "(private) A NBQ dispersion model",
      "topics": [
        "log.phi.nbq"
      ]
    },
    {
      "page": "ma.plot",
      "title": "(private) MA plot with differently expressed genes highlighted",
      "topics": [
        "ma.plot"
      ]
    },
    {
      "page": "make.disp",
      "title": "(private) Specify a dispersion model",
      "topics": [
        "make.disp"
      ]
    },
    {
      "page": "mv.line",
      "title": "(private) Overlay an estimated mean-variance line",
      "topics": [
        "mv.line"
      ]
    },
    {
      "page": "mv.line.fitted",
      "title": "(private) Overlay an estimated mean-variance line",
      "topics": [
        "mv.line.fitted"
      ]
    },
    {
      "page": "mv.line.nbp",
      "title": "(private) Overlay a NBP mean-variance line on an existing plot",
      "topics": [
        "mv.line.nbp"
      ]
    },
    {
      "page": "mv.plot",
      "title": "(private) Mean-variance plot",
      "topics": [
        "mv.plot"
      ]
    },
    {
      "page": "mv.points",
      "title": "(private) Highlight a subset of points on the mean-variance plot",
      "topics": [
        "mv.points"
      ]
    },
    {
      "page": "nb.glm.test",
      "title": "Fit Negative Binomial Regression Model and Test for a Regression Coefficient",
      "topics": [
        "nb.glm.test"
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    },
    {
      "page": "nbp.test",
      "title": "NBP Test for Differential Gene Expression from RNA-Seq Counts",
      "topics": [
        "nbp.test"
      ]
    },
    {
      "page": "nll.log.phi.fun",
      "title": "Negative profile conditional likelihood of the dispersion model",
      "topics": [
        "nll.log.phi.fun"
      ]
    },
    {
      "page": "optim.disp.apl",
      "title": "(private) Estimate the parameters in a dispersion model",
      "topics": [
        "optim.disp.apl"
      ]
    },
    {
      "page": "optim.disp.pl",
      "title": "(private) Estimate the parameters in a dispersion model",
      "topics": [
        "optim.disp.pl"
      ]
    },
    {
      "page": "phi.line",
      "title": "(private) Overlay an mean-dispersion line on an esimtated plot",
      "topics": [
        "phi.line"
      ]
    },
    {
      "page": "phi.line.fitted",
      "title": "(private) Overlay an estimated mean-dispersion line on an existing plot",
      "topics": [
        "phi.line.fitted"
      ]
    },
    {
      "page": "phi.line.nbp",
      "title": "(private) Overlay an estimated mean-dispersion line on an existing plot",
      "topics": [
        "phi.line.nbp"
      ]
    },
    {
      "page": "phi.plot",
      "title": "Plot estimated genewise NB2 dispersion parameter versus estimated mean",
      "topics": [
        "phi.plot"
      ]
    },
    {
      "page": "plot.nb.data",
      "title": "Boxplot and scatterplot matrix of relative frequencies (after normalization)",
      "topics": [
        "plot.nb.data"
      ]
    },
    {
      "page": "plot.nb.dispersion",
      "title": "Plot the estimated dispersion as a function of the preliminarily estimated mean relative frequencies",
      "topics": [
        "plot.nb.dispersion"
      ]
    },
    {
      "page": "plot.nbp",
      "title": "Diagnostic Plots for an NBP Object",
      "topics": [
        "plot.nbp"
      ]
    },
    {
      "page": "prepare.nb.data",
      "title": "Prepare the NB Data Structure for RNA-Seq Read Counts",
      "topics": [
        "prepare.nb.data"
      ]
    },
    {
      "page": "prepare.nbp",
      "title": "Prepare the Data Structure for Exact NB test for Two-Group Comparison",
      "topics": [
        "prepare.nbp"
      ]
    },
    {
      "page": "print.nb.data",
      "title": "Print summary of the nb counts",
      "topics": [
        "print.nb.data"
      ]
    },
    {
      "page": "print.nb.dispersion",
      "title": "Print the estimated dispersion model",
      "topics": [
        "print.nb.dispersion"
      ]
    },
    {
      "page": "print.nb.test",
      "title": "Print output from 'test.coefficient'",
      "topics": [
        "print.nb.test"
      ]
    },
    {
      "page": "print.nbp",
      "title": "Print summary of an NBP Object",
      "topics": [
        "print.nbp"
      ]
    },
    {
      "page": "smart.plot.new",
      "title": "(private) An alternative to plot.default() for plotting a large number of densely distributed points.",
      "topics": [
        "smart.plot.new"
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    },
    {
      "page": "smart.plot.old",
      "title": "(private) An alternative to plot.default() for plotting a large number of densely distributed points.",
      "topics": [
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    },
    {
      "page": "smart.points",
      "title": "(private) An alternative to point.default() for plotting a large number of densely distributed points.",
      "topics": [
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    },
    {
      "page": "test.coefficient",
      "title": "Large-sample Test for a Regression Coefficient in an Negative Binomial Regression Model",
      "topics": [
        "test.coefficient"
      ]
    },
    {
      "page": "thin.counts",
      "title": "(private) Thin (downsample) counts to make the effective library sizes equal.",
      "topics": [
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