EDASeq-package	EDASeq-package
barplot,BamFile-method	barplot-methods
barplot,BamFileList-method	barplot-methods
barplot,FastqFileList-method	barplot-methods
barplot-methods	barplot-methods
betweenLaneNormalization	betweenLaneNormalization-methods
betweenLaneNormalization,matrix-method	betweenLaneNormalization-methods
betweenLaneNormalization,SeqExpressionSet-method	betweenLaneNormalization-methods
betweenLaneNormalization-methods	betweenLaneNormalization-methods
biasBoxplot	biasBoxplot-methods
biasBoxplot,numeric,numeric,numeric-method	biasBoxplot-methods
biasBoxplot,numeric,numeric-method	biasBoxplot-methods
biasBoxplot-methods	biasBoxplot-methods
biasPlot	biasPlot-methods
biasPlot,matrix,numeric-method	biasPlot-methods
biasPlot,SeqExpressionSet,character-method	biasPlot-methods
biasPlot-methods	biasPlot-methods
boxplot,FastqQuality-method	boxplot-methods
boxplot,SeqExpressionSet-method	boxplot-methods
boxplot-methods	boxplot-methods
coerce,SeqExpressionSet,CountDataSet-method	SeqExpressionSet-class
counts,SeqExpressionSet-method	SeqExpressionSet-class
counts<-,SeqExpressionSet,ANY-method	SeqExpressionSet-class
EDASeq	EDASeq-package
exprs,SeqExpressionSet-method	SeqExpressionSet-class
exprs<-,SeqExpressionSet,ANY-method	SeqExpressionSet-class
initialize,SeqExpressionSet-method	SeqExpressionSet-class
MDPlot	MDPlot-methods
MDPlot,matrix,numeric-method	MDPlot-methods
MDPlot,SeqExpressionSet,numeric-method	MDPlot-methods
MDPlot-methods	MDPlot-methods
meanVarPlot	meanVarPlot-methods
meanVarPlot,SeqExpressionSet-method	meanVarPlot-methods
meanVarPlot-methods	meanVarPlot-methods
newSeqExpressionSet	newSeqExpressionSet
normCounts	SeqExpressionSet-class
normCounts,SeqExpressionSet-method	SeqExpressionSet-class
normCounts<-	SeqExpressionSet-class
normCounts<-,SeqExpressionSet,ANY-method	SeqExpressionSet-class
normCounts<-,SeqExpressionSet-method	SeqExpressionSet-class
offst	SeqExpressionSet-class
offst,SeqExpressionSet-method	SeqExpressionSet-class
offst<-	SeqExpressionSet-class
offst<-,SeqExpressionSet,ANY-method	SeqExpressionSet-class
offst<-,SeqExpressionSet-method	SeqExpressionSet-class
plot,BamFileList,FastqFileList-method	plot-methods
plot-methods	plot-methods
plotNtFrequency	plotNtFrequency-methods
plotNtFrequency,BamFile-method	plotNtFrequency-methods
plotNtFrequency,ShortRead-method	plotNtFrequency-methods
plotNtFrequency-methods	plotNtFrequency-methods
plotPCA	plotPCA-methods
plotPCA,matrix-method	plotPCA-methods
plotPCA,SeqExpressionSet-method	plotPCA-methods
plotPCA-methods	plotPCA-methods
plotQuality	plotQuality-methods
plotQuality,BamFile-method	plotQuality-methods
plotQuality,BamFileList-method	plotQuality-methods
plotQuality,FastqFileList-method	plotQuality-methods
plotQuality-methods	plotQuality-methods
plotRLE	plotRLE-methods
plotRLE,matrix-method	plotRLE-methods
plotRLE,SeqExpressionSet-method	plotRLE-methods
plotRLE-methods	plotRLE-methods
SeqExpressionSet-class	SeqExpressionSet-class
withinLaneNormalization	withinLaneNormalization-methods
withinLaneNormalization,matrix,numeric-method	withinLaneNormalization-methods
withinLaneNormalization,SeqExpressionSet,character-method	withinLaneNormalization-methods
withinLaneNormalization-methods	withinLaneNormalization-methods
yeastGC	yeastGC
yeastLength	yeastLength
