Differential gene expression analysis based on the negative binomial distribution


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Documentation for package ‘DESeq2’ version 1.2.10

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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
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 from variance-stabilized data
removeResults Extract results from a DESeq analysis
replaceOutliersWithTrimmedMean Replace outliers with trimmed mean
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