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).

Author
Davide Risso [aut, cre, cph], Sandrine Dudoit [aut], Ludwig Geistlinger [ctb]
Date of publication
None
Maintainer
Davide Risso <risso.davide@gmail.com>
License
Artistic-2.0
Version
2.8.0
URLs

View on Bioconductor

Man pages

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

Files in this package

EDASeq/DESCRIPTION
EDASeq/NAMESPACE
EDASeq/R
EDASeq/R/AllClasses.R
EDASeq/R/AllGenerics.R
EDASeq/R/functions.R
EDASeq/R/getLengthAndGC.R
EDASeq/R/methods-BamFileList.R
EDASeq/R/methods-FastqFileList.R
EDASeq/R/methods-Others.R
EDASeq/R/methods-SeqExpressionSet.R
EDASeq/build
EDASeq/build/vignette.rds
EDASeq/data
EDASeq/data/yeastGC.rda
EDASeq/data/yeastLength.rda
EDASeq/inst
EDASeq/inst/CITATION
EDASeq/inst/NEWS
EDASeq/inst/doc
EDASeq/inst/doc/EDASeq.R
EDASeq/inst/doc/EDASeq.Rnw
EDASeq/inst/doc/EDASeq.pdf
EDASeq/man
EDASeq/man/EDASeq-package.Rd
EDASeq/man/MDPlot-methods.Rd
EDASeq/man/SeqExpressionSet-class.Rd
EDASeq/man/barplot-methods.Rd
EDASeq/man/betweenLaneNormalization-methods.Rd
EDASeq/man/biasBoxplot-methods.Rd
EDASeq/man/biasPlot-methods.Rd
EDASeq/man/boxplot-methods.Rd
EDASeq/man/getGeneLengthAndGCContent.Rd
EDASeq/man/meanVarPlot-methods.Rd
EDASeq/man/newSeqExpressionSet.Rd
EDASeq/man/plot-methods.Rd
EDASeq/man/plotNtFrequency-methods.Rd
EDASeq/man/plotPCA-methods.Rd
EDASeq/man/plotQuality-methods.Rd
EDASeq/man/plotRLE-methods.Rd
EDASeq/man/withinLaneNormalization-methods.Rd
EDASeq/man/yeastGC.Rd
EDASeq/man/yeastLength.Rd
EDASeq/tests
EDASeq/tests/plotPCA.R
EDASeq/vignettes
EDASeq/vignettes/EDASeq.Rnw