# Digital gene expresion analysis based on the negative binomial distribution

## Documentation for package ‘DESeq’ version 1.0.6

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

adjustScvForBias | Adjust an SCV value for the bias arising when it is calculated from unbiased estimates of mean and variance.
conditions | Accessor function for the conditions information in a CountDataSet
CountDataSet-class | Class "CountDataSet" - a container for count data from HTS experiments
counts | Accessor for the 'counts' slot of a CountDataSet object.
estimateSizeFactors | Estimate the size factors for a CountDataSet
estimateSizeFactorsForMatrix | Low-level function to estimate size factors with robust regression.
estimateVarianceFunctionForMatrix | Lower-level function to estimate a raw variance function.
estimateVarianceFunctions | Estimate the variance functions for a CountDataSet.
getBaseMeansAndVariances | Perform row-wise estimates of base-level means and variances for count data.
getVarianceStabilizedData | Perform a variance stabilising transformation (VST) on the count data
makeExampleCountDataSet | make a simple example CountDataSet with random data
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.
newCountDataSet | Create a CountDataSet object
rawVarFunc | Accessor for raw variance functions
rawVarFuncTable | Accessor function for the slot rawVarFuncTable of the class CountDataSet
residualsEcdfPlot | Produce a diagnostic plot to check the fit of a raw variance function.
residualsEcdfPlotFromDiagnostics | Produce a diagnostic plot to check the fit of a raw variance function.
scvPlot | Produces a diagnostic plot with the variance estimates, given as squared coefficients of variation (SCV)
sizeFactors | Accessor functions for the sizeFactors information in a CountDataSet
sizeFactors<- | Accessor functions for the sizeFactors information in a CountDataSet
varianceFitDiagnostics | Generate a data frame with diagnostic information on the fit of a base variance function.
varianceFitDiagnosticsForMatrix | A lower-level function to get fit diagnostics