# Digital gene expresion analysis based on the negative binomial distribution

## Documentation for package ‘DESeq’ version 1.2.1

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

## Help Pages

adjustScvForBias | Adjust an SCV value for the bias arising when it is calculated from
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.
estimatePooledVarianceFunctionForMatrix | Lower-level functions to estimate a raw variance function.
estimateSizeFactors | Estimate the size factors for a CountDataSet
estimateSizeFactorsForMatrix | Low-level function to estimate size factors with robust regression.
estimateVarianceFunctionForMatrix | Lower-level functions 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
getRawScvDistanceMatrix | Calculates a matrix of "distances" between samples
getRawScvForSamplePair | for a pair of samples, calculate the average raw SCV between them, as a
getVarianceStabilizedData | Perform a variance stabilising transformation (VST) on the count data
makeExampleCountDataSet | make a simple example CountDataSet with random data
nbinomFitGLM | Fit a generalized linear model (GLM) for each gene.
nbinomGLMsForMatrix | Fit negative binomial GLMs to a count matrix.
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
nbkd.sf | GLM family for a negative binomial with known dispersion and log link
newCountDataSet | Create a CountDataSet object
rawVarFunc | Accessor for raw variance functions
rawVarFuncTable | Accessor functions for the slot rawVarFuncTable of the class
rawVarFuncTable<- | Accessor functions for the slot rawVarFuncTable of the class
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
sizeFactors | Accessor functions for the sizeFactors information in a CountDataSet
sizeFactors<- | Accessor functions for the sizeFactors information in a CountDataSet
varAdjFactors | Defunct function. Do not use.
varAdjFactors<- | Defunct function. Do not use.
varianceFitDiagnostics | Generate a data frame with diagnostic information on the fit of a base
varianceFitDiagnosticsForMatrix | A lower-level function to get fit diagnostics