# Exploratory analysis and differential expression for RNA-seq data

## Documentation for package ‘NOISeq’ version 2.28.0

- 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