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NOISeq (version 2.16.0)

Exploratory analysis and differential expression for RNA-seq data

Description

Analysis of RNA-seq expression data or other similar kind of data. Exploratory plots to evualuate saturation, count distribution, expression per chromosome, type of detected features, features length, etc. Differential expression between two experimental conditions with no parametric assumptions.

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Version

Version

2.16.0

License

Artistic-2.0

Maintainer

Sonia Tarazona

Last Published

February 15th, 2017

Functions in NOISeq (2.16.0)

Exploratory_Plots

Exploratory plots for expression data.
example

Example of objects used and created by the NOISeq package
noiseqbio

Differential expression method for biological replicates
Normalization

Normalization methods
Biodetection

Biodetection class
ARSyNseq

ASCA Removal of Systematic Noise on Seq data
readData

Creating an object of eSet class
FilterLowCounts

Methods to filter out low count features
Saturation

Saturation class
GCbias

GCbias class
Differential expression plots

Plotting differential expression results
PCA.GENES

Principal Component Analysis
degenes

Recovering differencially expressed features.
Output

Output class of NOISeq
PCA

PCA class
QCreport

Quality Control report for expression data
CD

CD class
CountsBio

CountsBio class
myCounts

Class myCounts
noiseq

Differential expression method for technical replicates or no replicates at all
Data_Exploration

Exploration of expression data.
Data2Save

Saving data generated for exploratory plots.
lengthbias

lengthbias class
Marioni

Marioni's dataset