Exploratory analysis and differential expression for RNA-seq data

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Documentation for package ‘NOISeq’ version 2.53.0

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

Help Pages

addData	Creating an object of eSet class
ARSyNseq	ASCA Removal of Systematic Noise on Seq data
arsynseq	ASCA Removal of Systematic Noise on Seq data
Biodetection	Biodetection class
Biodetection-class	Biodetection class
CD	CD class
CD-class	CD class
CountsBio	CountsBio class
CountsBio-class	CountsBio class
dat	Exploration of expression data.
dat2save	Saving data generated for exploratory plots.
dat2save-method	Biodetection class
dat2save-method	CD class
dat2save-method	CountsBio class
dat2save-method	GCbias class
dat2save-method	lengthbias class
dat2save-method	PCA class
dat2save-method	Saturation class
DE.plot	Plotting differential expression results
degenes	Recovering differencially expressed features.
explo.plot	Exploratory plots for expression data.
explo.plot-method	Biodetection class
explo.plot-method	CD class
explo.plot-method	CountsBio class
explo.plot-method	GCbias class
explo.plot-method	lengthbias class
explo.plot-method	PCA class
explo.plot-method	Saturation class
filtered.data	Methods to filter out low count features
GCbias	GCbias class
GCbias-class	GCbias class
lengthbias	lengthbias class
lengthbias-class	lengthbias class
mybiotypes	Marioni's dataset
mychroms	Marioni's dataset
myCounts	Class myCounts
mycounts	Marioni's dataset
myCounts-class	Class myCounts
mydata	Example of objects used and created by the NOISeq package
myfactors	Marioni's dataset
mygc	Marioni's dataset
mylength	Marioni's dataset
mynoiseq	Example of objects used and created by the NOISeq package
noiseq	Differential expression method for technical replicates or no replicates at all
noiseqbio	Differential expression method for biological replicates
Output	Output class of NOISeq
Output-class	Output class of NOISeq
PCA	PCA class
PCA-class	PCA class
PCA.GENES	Principal Component Analysis
QCreport	Quality Control report for expression data
readData	Creating an object of eSet class
rpkm	Normalization methods
Saturation	Saturation class
saturation	Saturation class
Saturation-class	Saturation class
show-method	Biodetection class
show-method	CD class
show-method	CountsBio class
show-method	GCbias class
show-method	lengthbias class
show-method	Output class of NOISeq
show-method	PCA class
show-method	Saturation class
tmm	Normalization methods
uqua	Normalization methods