EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq

Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).

AuthorDavide Risso [aut, cre, cph], Sandrine Dudoit [aut], Ludwig Geistlinger [ctb]
Date of publicationNone
MaintainerDavide Risso <risso.davide@gmail.com>

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

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