Differential gene expression analysis based on the negative binomial distribution


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Documentation for package ‘DESeq’ version 1.39.0

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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.
conditions-method Accessor functions for the 'conditions' information in a CountDataSet object.
conditions<--method 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.
counts-method Accessors for the 'counts' slot of a CountDataSet object.
counts<--method Accessors for the 'counts' slot of a CountDataSet object.
dispTable Accessor function for the dispTable information in a CountDataSet
dispTable-method Accessor function for the dispTable information in a CountDataSet
estimateDispersions Estimate and fit dispersions for a CountDataSet.
estimateDispersions-method Estimate and fit dispersions for a CountDataSet.
estimateSizeFactors Estimate the size factors for a CountDataSet
estimateSizeFactors-method 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.
sizeFactors-method Accessor functions for the 'sizeFactors' information in a CountDataSet object.
sizeFactors<--method Accessor functions for the 'sizeFactors' information in a CountDataSet object.
varianceFitDiagnostics REMOVED
varianceStabilizingTransformation Apply a variance stabilizing transformation (VST) to the count data