CountDataSet-class      Class "CountDataSet" - a container for count
                        data from HTS experiments
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.
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