Exploratory Data Analysis and Normalization for RNA-Seq


[Up] [Top]

Documentation for package ‘EDASeq’ version 2.39.0

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'
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