# Differential gene expression analysis based on the negative binomial distribution

## Documentation for package ‘DESeq2’ version 1.18.1

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

## Help Pages

DESeq2-package | DESeq2 package for differential analysis of count data
coef | Extract a matrix of model coefficients/standard errors
coef.DESeqDataSet | Extract a matrix of model coefficients/standard errors
collapseReplicates | Collapse technical replicates in a RangedSummarizedExperiment or DESeqDataSet
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 (a.k.a. Gamma-Poisson) distribution
DESeqDataSet | DESeqDataSet object and constructors
DESeqDataSet-class | DESeqDataSet object and constructors
DESeqDataSetFromHTSeqCount | DESeqDataSet object and constructors
DESeqDataSetFromMatrix | DESeqDataSet object and constructors
DESeqDataSetFromTximport | DESeqDataSet object and constructors
DESeqResults | DESeqResults object and constructor
DESeqResults-class | DESeqResults object and constructor
DESeqTransform | DESeqTransform object and constructor
DESeqTransform-class | DESeqTransform object and constructor
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.
estimateBetaPriorVar | Steps for estimating the beta prior variance
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
estimateDispersionsPriorVar | Low-level functions to fit dispersion estimates
estimateMLEForBetaPriorVar | Steps for estimating the beta prior variance
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.
fpkm | FPKM: fragments per kilobase per million mapped fragments
fpm | FPM: fragments per million mapped fragments
getVarianceStabilizedData | Apply a variance stabilizing transformation (VST) to the count data
lfcShrink | Shrink log2 fold changes
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.
normalizeGeneLength | Normalize for gene length
normTransform | Normalized counts transformation
plotCounts | Plot of normalized counts for a single gene
plotDispEsts | Plot dispersion estimates
plotDispEsts-method | Plot dispersion estimates
plotMA | MA-plot from base means and log fold changes
plotMA-method | MA-plot from base means and log fold changes
plotPCA | Sample PCA plot for transformed data
plotPCA-method | Sample PCA plot for transformed data
plotSparsity | Sparsity plot
priorInfo | Accessors for the 'priorInfo' slot of a DESeqResults object.
priorInfo-method | Accessors for the 'priorInfo' slot of a DESeqResults object.
priorInfo<- | Accessors for the 'priorInfo' slot of a DESeqResults object.
priorInfo<--method | Accessors for the 'priorInfo' slot of a DESeqResults object.
removeResults | Extract results from a DESeq analysis
replaceOutliers | Replace outliers with trimmed mean
replaceOutliersWithTrimmedMean | Replace outliers with trimmed mean
results | Extract results from a DESeq analysis
resultsNames | Extract results from a DESeq analysis
rlog | Apply a 'regularized log' transformation
rlogTransformation | Apply a 'regularized log' transformation
show | Show method for DESeqResults objects
show-method | Show method for DESeqResults objects
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.
summary | Summarize DESeq results
summary.DESeqResults | Summarize DESeq results
unmix | Unmix samples using loss in a variance stabilized space
varianceStabilizingTransformation | Apply a variance stabilizing transformation (VST) to the count data
vst | Quickly estimate dispersion trend and apply a variance stabilizing transformation