DESeq                   Differential expression analysis based on the
                        Negative Binomial (a.k.a. Gamma-Poisson)
                        distribution
DESeq2-package          DESeq2 package for differential analysis of
                        count data
DESeqDataSet-class      DESeqDataSet object and constructors
DESeqResults-class      DESeqResults object and constructor
DESeqTransform-class    DESeqTransform object and constructor
coef.DESeqDataSet       Extract a matrix of model coefficients/standard
                        errors
collapseReplicates      Collapse technical replicates in a
                        RangedSummarizedExperiment or DESeqDataSet
counts,DESeqDataSet-method
                        Accessors for the 'counts' slot of a
                        DESeqDataSet object.
design,DESeqDataSet-method
                        Accessors for the 'design' slot of a
                        DESeqDataSet object.
dispersionFunction      Accessors for the 'dispersionFunction' slot of
                        a DESeqDataSet object.
dispersions             Accessor functions for the dispersion estimates
                        in a DESeqDataSet object.
estimateBetaPriorVar    Steps for estimating the beta prior variance
estimateDispersions,DESeqDataSet-method
                        Estimate the dispersions for a DESeqDataSet
estimateDispersionsGeneEst
                        Low-level functions to fit dispersion estimates
estimateSizeFactors,DESeqDataSet-method
                        Estimate the size factors for a 'DESeqDataSet'
estimateSizeFactorsForMatrix
                        Low-level function to estimate size factors
                        with robust regression.
fpkm                    FPKM: fragments per kilobase per million mapped
                        fragments
fpm                     FPM: fragments per million mapped fragments
integrateWithSingleCell
                        Integrate bulk DE results with Bioconductor
                        single-cell RNA-seq datasets
lfcShrink               Shrink log2 fold changes
makeExampleDESeqDataSet
                        Make a simulated DESeqDataSet
nbinomLRT               Likelihood ratio test (chi-squared test) for
                        GLMs
nbinomWaldTest          Wald test for the GLM coefficients
normTransform           Normalized counts transformation
normalizationFactors    Accessor functions for the normalization
                        factors in a DESeqDataSet object.
normalizeGeneLength     Normalize for gene length
plotCounts              Plot of normalized counts for a single gene
plotDispEsts            Plot dispersion estimates
plotMA                  MA-plot from base means and log fold changes
plotPCA                 Sample PCA plot for transformed data
plotSparsity            Sparsity plot
priorInfo               Accessors for the 'priorInfo' slot of a
                        DESeqResults object.
replaceOutliers         Replace outliers with trimmed mean
results                 Extract results from a DESeq analysis
rlog                    Apply a 'regularized log' transformation
show,DESeqResults-method
                        Show method for DESeqResults objects
sizeFactors,DESeqDataSet-method
                        Accessor functions for the 'sizeFactors'
                        information in a DESeqDataSet object.
summary,DESeqResults-method
                        Summarize DESeq results
unmix                   Unmix samples using loss in a variance
                        stabilized space
varianceStabilizingTransformation
                        Apply a variance stabilizing transformation
                        (VST) to the count data
vst                     Quickly estimate dispersion trend and apply a
                        variance stabilizing transformation