# Differential gene expression analysis based on the negative binomial distribution

## Documentation for package ‘DESeq’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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