Package fr.ens.biologie.genomique.eoulsan.modules.diffana

This package contain all the classes related to the differential analysis step.

Since:

1.0

Class Summary

Class	Description
DESeq2	This class contains methods to run the differential analysis module DESeq2.
DESeq2Module	Class to run the differential analysis with DEseq2
DiffAna	This class create and launch a R script to compute differential analysis.
DiffAnaModule	This class define the module of differential analysis in local mode.
DiffanaResultsAnnotationModule	This class define a module that create annotated expression files in TSV, ODS or XLSX format.
Normalization	This class create and launch an R script to compute normalisation of expression data
NormalizationModule	This class define the module for normalization
RModuleCommonConfiguration	This class define common methods used for the configuration of the step of the package.

Enum Summary

Enum	Description
DESeq2.FitType	Enum for the fitType option in DESeq2 related to the dispersion estimation.
DESeq2.SizeFactorsType	Enum for the sizeFactorsType option in DESeq2 related to the estimation of the size factor.
DESeq2.StatisticTest	Enum for the statisticTest option in DESeq2 related to the statistic test to be used during the differential expression analysis
DiffAna.DispersionFitType	Dispersion estimation fitType enum for DESeq differential analysis
DiffAna.DispersionMethod	Dispersion estimation method enum for DESeq differential analysis
DiffAna.DispersionSharingMode	Dispersion estimation sharingMode enum for DESeq differential analysis