Exploratory analysis and differential expression for RNA-seq data

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Documentation for package ‘NOISeq’ version 2.22.0

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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