# Differential gene expression analysis based on the negative binomial distribution

## Documentation for package ‘DESeq2’ version 1.0.19

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

## Help Pages

counts | Accessors for the 'counts' slot of a DESeqDataSet object.
counts-method | Accessors for the 'counts' slot of a DESeqDataSet object.
counts<--method | Accessors for the 'counts' slot of a DESeqDataSet object.
DESeq | Differential expression analysis based on the negative binomial distribution
DESeqDataSet | DESeqDataSet object and constructors
DESeqDataSet-class | DESeqDataSet object and constructors
DESeqDataSetFromHTSeqCount | DESeqDataSet object and constructors
DESeqDataSetFromMatrix | DESeqDataSet object and constructors
design | Accessors for the 'design' slot of a DESeqDataSet object.
design-method | Accessors for the 'design' slot of a DESeqDataSet object.
design<--method | Accessors for the 'design' slot of a DESeqDataSet object.
dispersionFunction | Accessors for the 'dispersionFunction' slot of a DESeqDataSet object.
dispersionFunction-method | Accessors for the 'dispersionFunction' slot of a DESeqDataSet object.
dispersionFunction<- | Accessors for the 'dispersionFunction' slot of a DESeqDataSet object.
dispersionFunction<--method | Accessors for the 'dispersionFunction' slot of a DESeqDataSet object.
dispersions | Accessor functions for the dispersion estimates in a DESeqDataSet object.
dispersions-method | Accessor functions for the dispersion estimates in a DESeqDataSet object.
dispersions<- | Accessor functions for the dispersion estimates in a DESeqDataSet object.
dispersions<--method | Accessor functions for the dispersion estimates in a DESeqDataSet object.
estimateDispersions | Estimate the dispersions for a DESeqDataSet
estimateDispersions-method | Estimate the dispersions for a DESeqDataSet
estimateDispersionsFit | Low-level functions to fit dispersion estimates
estimateDispersionsGeneEst | Low-level functions to fit dispersion estimates
estimateDispersionsMAP | Low-level functions to fit dispersion estimates
estimateSizeFactors | Estimate the size factors for a DESeqDataSet
estimateSizeFactors-method | Estimate the size factors for a DESeqDataSet
estimateSizeFactorsForMatrix | Low-level function to estimate size factors with robust regression.
getVarianceStabilizedData | Apply a variance stabilizing transformation (VST) to the count data
makeExampleDESeqDataSet | Make a simulated DESeqDataSet
nbinomLRT | Likelihood ratio test (chi-squared test) for GLMs
nbinomWaldTest | Wald test for the GLM coefficients
normalizationFactors | Accessor functions for the normalization factors in a DESeqDataSet object.
normalizationFactors-method | Accessor functions for the normalization factors in a DESeqDataSet object.
normalizationFactors<- | Accessor functions for the normalization factors in a DESeqDataSet object.
normalizationFactors<--method | Accessor functions for the normalization factors in a DESeqDataSet object.
plotDispEsts | Plot dispersion estimates
plotMA | MA-plot from base means and log fold changes
plotPCA | Sample PCA plot from variance-stabilized data
removeResults | Extract results from a DESeq analysis
results | Extract results from a DESeq analysis
resultsNames | Extract results from a DESeq analysis
rlogData | Apply a 'regularized log' transformation
rlogTransformation | Apply a 'regularized log' transformation
sizeFactors | Accessor functions for the 'sizeFactors' information in a DESeqDataSet object.
sizeFactors-method | Accessor functions for the 'sizeFactors' information in a DESeqDataSet object.
sizeFactors<--method | Accessor functions for the 'sizeFactors' information in a DESeqDataSet object.
varianceStabilizingTransformation | Apply a variance stabilizing transformation (VST) to the count data