Package fr.ens.biologie.genomique.eoulsan.modules.diffana
package fr.ens.biologie.genomique.eoulsan.modules.diffana
This package contain all the classes related to the differential analysis step.
- Since:
- 1.0
-
ClassDescriptionThis class contains methods to run the differential analysis module DESeq2.Class to run the differential analysis with DEseq2This class contains DESeq2 module parameters.Enum for the fitType option in DESeq2 related to the dispersion estimation.Enum for the sizeFactorsType option in DESeq2 related to the estimation of the size factor.Enum for the statisticTest option in DESeq2 related to the statistic test to be used during the differential expression analysisThis class create and launch a R script to compute differential analysis.Dispersion estimation fitType enum for DESeq differential analysisDispersion estimation method enum for DESeq differential analysisDispersion estimation sharingMode enum for DESeq differential analysisThis class define the module of differential analysis in local mode.This class define a module that create annotated expression files in TSV, ODS or XLSX format.This class allow to execute easy contrasts 1.This class allow to execute easy contrasts 2.This class create and launch an R script to compute normalisation of expression dataThis class define the module for normalizationThis class define common methods used for the configuration of the step of the package.