Differential gene expression analysis based on the negative binomial distribution

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Documentation for package ‘DESeq2’ version 1.38.3

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

Help Pages

DESeq2-package	DESeq2 package for differential analysis of count data
coef.DESeqDataSet	Extract a matrix of model coefficients/standard errors
collapseReplicates	Collapse technical replicates in a RangedSummarizedExperiment or DESeqDataSet
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-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-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-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
integrateWithSingleCell	Integrate bulk DE results with Bioconductor single-cell RNA-seq datasets
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-method	Show method for DESeqResults objects
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-method	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