# Exploratory Data Analysis and Normalization for RNA-Seq

## Documentation for package ‘EDASeq’ version 2.16.3

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

## Help Pages

EDASeq-package | Exploratory Data Analysis and Normalization for RNA-Seq data
barplot-method | Methods for Function 'barplot' in Package 'EDASeq'
barplot-methods | Methods for Function 'barplot' in Package 'EDASeq'
betweenLaneNormalization | Methods for Function 'betweenLaneNormalization' in Package 'EDASeq'
betweenLaneNormalization-method | Methods for Function 'betweenLaneNormalization' in Package 'EDASeq'
betweenLaneNormalization-methods | Methods for Function 'betweenLaneNormalization' in Package 'EDASeq'
biasBoxplot | Methods for Function 'biasBoxplot' in Package 'EDASeq'
biasBoxplot-method | Methods for Function 'biasBoxplot' in Package 'EDASeq'
biasBoxplot-methods | Methods for Function 'biasBoxplot' in Package 'EDASeq'
biasPlot | Methods for Function 'biasPlot' in Package 'EDASeq'
biasPlot-method | Methods for Function 'biasPlot' in Package 'EDASeq'
biasPlot-methods | Methods for Function 'biasPlot' in Package 'EDASeq'
boxplot-method | Methods for Function 'boxplot' in Package 'EDASeq'
boxplot-methods | Methods for Function 'boxplot' in Package 'EDASeq'
coerce-method | "SeqExpressionSet" class for collections of short reads
counts-method | "SeqExpressionSet" class for collections of short reads
counts<--method | "SeqExpressionSet" class for collections of short reads
EDASeq | Exploratory Data Analysis and Normalization for RNA-Seq data
exprs-method | "SeqExpressionSet" class for collections of short reads
exprs<--method | "SeqExpressionSet" class for collections of short reads
getGeneLengthAndGCContent | Get gene length and GC-content
initialize-method | "SeqExpressionSet" class for collections of short reads
MDPlot | Methods for Function 'MDPlot' in Package 'EDASeq'
MDPlot-method | Methods for Function 'MDPlot' in Package 'EDASeq'
MDPlot-methods | Methods for Function 'MDPlot' in Package 'EDASeq'
meanVarPlot | Methods for Function 'meanVarPlot' in Package 'EDASeq'
meanVarPlot-method | Methods for Function 'meanVarPlot' in Package 'EDASeq'
meanVarPlot-methods | Methods for Function 'meanVarPlot' in Package 'EDASeq'
newSeqExpressionSet | Function to create a new 'SeqExpressionSet' object.
normCounts | "SeqExpressionSet" class for collections of short reads
normCounts-method | "SeqExpressionSet" class for collections of short reads
normCounts<- | "SeqExpressionSet" class for collections of short reads
normCounts<--method | "SeqExpressionSet" class for collections of short reads
offst | "SeqExpressionSet" class for collections of short reads
offst-method | "SeqExpressionSet" class for collections of short reads
offst<- | "SeqExpressionSet" class for collections of short reads
offst<--method | "SeqExpressionSet" class for collections of short reads
plot-method | Methods for Function 'plot' in Package 'EDASeq'
plot-methods | Methods for Function 'plot' in Package 'EDASeq'
plotNtFrequency | Methods for Function 'plotNtFrequency' in Package 'EDASeq'
plotNtFrequency-method | Methods for Function 'plotNtFrequency' in Package 'EDASeq'
plotNtFrequency-methods | Methods for Function 'plotNtFrequency' in Package 'EDASeq'
plotPCA | Methods for Function 'plotPCA' in Package 'EDASeq'
plotPCA-method | Methods for Function 'plotPCA' in Package 'EDASeq'
plotPCA-methods | Methods for Function 'plotPCA' in Package 'EDASeq'
plotQuality | Methods for Function 'plotQuality' in Package 'EDASeq'
plotQuality-method | Methods for Function 'plotQuality' in Package 'EDASeq'
plotQuality-methods | Methods for Function 'plotQuality' in Package 'EDASeq'
plotRLE | Methods for Function 'plotRLE' in Package 'EDASeq'
plotRLE-method | Methods for Function 'plotRLE' in Package 'EDASeq'
plotRLE-methods | Methods for Function 'plotRLE' in Package 'EDASeq'
SeqExpressionSet-class | "SeqExpressionSet" class for collections of short reads
withinLaneNormalization | Methods for Function 'withinLaneNormalization' in Package 'EDASeq'
withinLaneNormalization-method | Methods for Function 'withinLaneNormalization' in Package 'EDASeq'
withinLaneNormalization-methods | Methods for Function 'withinLaneNormalization' in Package 'EDASeq'
yeastGC | GC-content of _S. Cerevisiae_ genes
yeastLength | Length of _S. Cerevisiae_ genes