EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq
Version 2.10.0

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]
Bioconductor views DifferentialExpression Preprocessing QualityControl RNASeq Sequencing
Date of publicationNone
MaintainerDavide Risso <risso.davide@gmail.com>
LicenseArtistic-2.0
Version2.10.0
URL https://github.com/drisso/EDASeq
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("EDASeq")

Getting started

Package overview

Popular man pages

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'
plotPCA-methods: Methods for Function 'plotPCA' in Package 'EDASeq'
plotRLE-methods: Methods for Function 'plotRLE' in Package 'EDASeq'
yeastGC: GC-content of _S. Cerevisiae_ genes
See all...

All man pages Function index File listing

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

Functions

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/functions.R
R/getLengthAndGC.R
R/methods-BamFileList.R
R/methods-FastqFileList.R
R/methods-Others.R
R/methods-SeqExpressionSet.R
build
build/vignette.rds
data
data/yeastGC.rda
data/yeastLength.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/EDASeq.R
inst/doc/EDASeq.Rnw
inst/doc/EDASeq.pdf
man
man/EDASeq-package.Rd
man/MDPlot-methods.Rd
man/SeqExpressionSet-class.Rd
man/barplot-methods.Rd
man/betweenLaneNormalization-methods.Rd
man/biasBoxplot-methods.Rd
man/biasPlot-methods.Rd
man/boxplot-methods.Rd
man/getGeneLengthAndGCContent.Rd
man/meanVarPlot-methods.Rd
man/newSeqExpressionSet.Rd
man/plot-methods.Rd
man/plotNtFrequency-methods.Rd
man/plotPCA-methods.Rd
man/plotQuality-methods.Rd
man/plotRLE-methods.Rd
man/withinLaneNormalization-methods.Rd
man/yeastGC.Rd
man/yeastLength.Rd
tests
tests/getLengthAndGC.R
tests/plots.R
vignettes
vignettes/EDASeq.Rnw
EDASeq documentation built on May 20, 2017, 9:36 p.m.

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