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 DEseq2DiffAna 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 dataNormalizationModule This class define the module for normalizationRModuleCommonConfiguration 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 analysisDiffAna.DispersionFitType Dispersion estimation fitType enum for DESeq differential analysisDiffAna.DispersionMethod Dispersion estimation method enum for DESeq differential analysisDiffAna.DispersionSharingMode Dispersion estimation sharingMode enum for DESeq differential analysis