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

adjustScvForBiasAdjust an SCV value for the bias arising when it is...
conditionsAccessor functions for the 'conditions' information in a...
CountDataSet-classClass "CountDataSet" - a container for count data from HTS...
countsAccessors for the 'counts' slot of a CountDataSet object.
dispTableAccessor function for the dispTable information in a...
estimateDispersionsEstimate and fit dispersions for a CountDataSet.
estimateSizeFactorsEstimate the size factors for a CountDataSet
estimateSizeFactorsForMatrixLow-level function to estimate size factors with robust...
estimateVarianceFunctionsREMOVED
fitInfoAccessor function for the fitInfo objects in a CountDataSet
fitNbinomGLMsFit a generalized linear model (GLM) for each gene.
fitNbinomGLMsForMatrixFit negative binomial GLMs to a count matrix.
getBaseMeansAndVariancesPerform row-wise estimates of base-level means and variances...
getVarianceStabilizedDataApply a variance stabilizing transformation (VST) to the...
makeExampleCountDataSetmake a simple example CountDataSet with random data
nbinomGLMTestPerform chi-squared tests comparing two sets of GLM fits
nbinomTestTest for differences between the base means for two...
nbinomTestForMatricesPerform row-wise tests for differences between the base means...
nbkd.sfGLM family for a negative binomial with known dispersion and...
newCountDataSetCreate a CountDataSet object
newCountDataSetFromHTSeqCountCreate a new CountDataSet from count files generated with...
plotDispEstsPlot dispersion estimates and fitted values
plotMAMakes a so-called "MA-plot"
plotPCASample PCA plot from variance-stabilized data
residualsEcdfPlotREMOVED
scvPlotREMOVED
sizeFactorsAccessor functions for the 'sizeFactors' information in a...
varianceFitDiagnosticsREMOVED
DESeq documentation built on Nov. 17, 2017, 12:51 p.m.