adjustScvForBias        Adjust an SCV value for the bias arising when
                        it is calculated from unbiased estimates of
                        mean and variance.
conditions              Accessor functions for the 'conditions'
                        information in a CountDataSet object.
CountDataSet-class      Class "CountDataSet" - a container for count
                        data from HTS experiments
counts                  Accessors for the 'counts' slot of a
                        CountDataSet object.
dispTable               Accessor function for the dispTable information
                        in a CountDataSet
estimateDispersions     Estimate and fit dispersions for a
                        CountDataSet.
estimateSizeFactors     Estimate the size factors for a CountDataSet
estimateSizeFactorsForMatrix
                        Low-level function to estimate size factors
                        with robust regression.
estimateVarianceFunctions
                        REMOVED
fitInfo                 Accessor function for the fitInfo objects in a
                        CountDataSet
fitNbinomGLMs           Fit a generalized linear model (GLM) for each
                        gene.
fitNbinomGLMsForMatrix
                        Fit negative binomial GLMs to a count matrix.
getBaseMeansAndVariances
                        Perform row-wise estimates of base-level means
                        and variances for count data.
getVarianceStabilizedData
                        Apply a variance stabilizing transformation
                        (VST) to the count data
makeExampleCountDataSet
                        make a simple example CountDataSet with random
                        data
nbinomGLMTest           Perform chi-squared tests comparing two sets of
                        GLM fits
nbinomTest              Test for differences between the base means for
                        two conditions
nbinomTestForMatrices   Perform row-wise tests for differences between
                        the base means of two count matrices.
nbkd.sf                 GLM family for a negative binomial with known
                        dispersion and log link with size factors
newCountDataSet         Create a CountDataSet object
newCountDataSetFromHTSeqCount
                        Create a new CountDataSet from count files
                        generated with htseq-count
plotDispEsts            Plot dispersion estimates and fitted values
plotMA                  Makes a so-called "MA-plot"
plotPCA                 Sample PCA plot from variance-stabilized data
residualsEcdfPlot       REMOVED
scvPlot                 REMOVED
sizeFactors             Accessor functions for the 'sizeFactors'
                        information in a CountDataSet object.
varianceFitDiagnostics
                        REMOVED
