Man pages for DESeq2
Differential gene expression analysis based on the negative binomial distribution

coefExtract a matrix of model coefficients/standard errors
collapseReplicatesCollapse technical replicates in a RangedSummarizedExperiment...
countsAccessors for the 'counts' slot of a DESeqDataSet object.
DESeqDifferential expression analysis based on the Negative...
DESeq2-packageDESeq2 package for differential analysis of count data
DESeqDataSetDESeqDataSet object and constructors
DESeqResultsDESeqResults object and constructor
DESeqTransformDESeqTransform object and constructor
designAccessors for the 'design' slot of a DESeqDataSet object.
dispersionFunctionAccessors for the 'dispersionFunction' slot of a DESeqDataSet...
dispersionsAccessor functions for the dispersion estimates in a...
estimateBetaPriorVarSteps for estimating the beta prior variance
estimateDispersionsEstimate the dispersions for a DESeqDataSet
estimateDispersionsGeneEstLow-level functions to fit dispersion estimates
estimateSizeFactorsEstimate the size factors for a 'DESeqDataSet'
estimateSizeFactorsForMatrixLow-level function to estimate size factors with robust...
fpkmFPKM: fragments per kilobase per million mapped fragments
fpmFPM: fragments per million mapped fragments
integrateWithSingleCellIntegrate bulk DE results with Bioconductor single-cell...
lfcShrinkShrink log2 fold changes
makeExampleDESeqDataSetMake a simulated DESeqDataSet
nbinomLRTLikelihood ratio test (chi-squared test) for GLMs
nbinomWaldTestWald test for the GLM coefficients
normalizationFactorsAccessor functions for the normalization factors in a...
normalizeGeneLengthNormalize for gene length
normTransformNormalized counts transformation
plotCountsPlot of normalized counts for a single gene
plotDispEstsPlot dispersion estimates
plotMAMA-plot from base means and log fold changes
plotPCASample PCA plot for transformed data
plotSparsitySparsity plot
priorInfoAccessors for the 'priorInfo' slot of a DESeqResults object.
replaceOutliersReplace outliers with trimmed mean
resultsExtract results from a DESeq analysis
rlogApply a 'regularized log' transformation
showShow method for DESeqResults objects
sizeFactorsAccessor functions for the 'sizeFactors' information in a...
summarySummarize DESeq results
unmixUnmix samples using loss in a variance stabilized space
varianceStabilizingTransformationApply a variance stabilizing transformation (VST) to the...
vstQuickly estimate dispersion trend and apply a variance...
DESeq2 documentation built on Feb. 22, 2021, 10 a.m.