checkExpDesignCompleteness	runDataProcessing
checkExpDesignCompleteness,RflomicsMAE-method	runDataProcessing
checkExpDesignCompleteness,RflomicsSE-method	runDataProcessing
createRflomicsMAE	createRflomicsMAE
ecoseed.df	ecoseed.df
ecoseed.mae	ecoseed.mae
filterDiffAnalysis	runDiffAnalysis
filterDiffAnalysis,RflomicsMAE-method	runDiffAnalysis
filterDiffAnalysis,RflomicsSE-method	runDiffAnalysis
generateExpressionContrast	generateExpressionContrast
generateExpressionContrast,RflomicsMAE-method	generateExpressionContrast
generateExpressionContrast,RflomicsSE-method	generateExpressionContrast
generateModelFormulae	generateModelFormulae
generateModelFormulae,RflomicsMAE-method	generateModelFormulae
generateReport	generateReport
generateReport,RflomicsMAE-method	generateReport
getAnalysis	getAnalysis
getAnalysis,RflomicsMAE-method	getAnalysis
getAnalysis,RflomicsSE-method	getAnalysis
getAnalyzedDatasetNames	getAnalysis
getAnalyzedDatasetNames,RflomicsMAE-method	getAnalysis
getAnnotAnalysesSummary	runAnnotationEnrichment
getAnnotAnalysesSummary,RflomicsMAE-method	runAnnotationEnrichment
getBatchFactors	RflomicsMAE-class
getBatchFactors,RflomicsMAE-method	RflomicsMAE-class
getBatchFactors,RflomicsSE-method	RflomicsSE-class
getBioFactors	RflomicsMAE-class
getBioFactors,RflomicsMAE-method	RflomicsMAE-class
getBioFactors,RflomicsSE-method	RflomicsSE-class
getCoeffNorm	runDataProcessing
getCoeffNorm,RflomicsMAE-method	runDataProcessing
getCoeffNorm,RflomicsSE-method	runDataProcessing
getCoExpAnalysesSummary	runCoExpression
getCoExpAnalysesSummary,RflomicsMAE-method	runCoExpression
getCoexpClusters	runCoExpression
getCoexpClusters,RflomicsMAE-method	runCoExpression
getCoexpClusters,RflomicsSE-method	runCoExpression
getCoexpSettings	runCoExpression
getCoexpSettings,RflomicsMAE-method	runCoExpression
getCoexpSettings,RflomicsSE-method	runCoExpression
getDatasetNames	RflomicsMAE-class
getDatasetNames,RflomicsMAE-method	RflomicsMAE-class
getDatasetNames,RflomicsSE-method	RflomicsSE-class
getDEList	runDiffAnalysis
getDEList,RflomicsMAE-method	runDiffAnalysis
getDEList,RflomicsSE-method	runDiffAnalysis
getDEMatrix	runDiffAnalysis
getDEMatrix,RflomicsMAE-method	runDiffAnalysis
getDEMatrix,RflomicsSE-method	runDiffAnalysis
getDesignMat	RflomicsMAE-class
getDesignMat,RflomicsMAE-method	RflomicsMAE-class
getDesignMat,RflomicsSE-method	RflomicsSE-class
getDiffAnalysesSummary	runDiffAnalysis
getDiffAnalysesSummary,RflomicsMAE-method	runDiffAnalysis
getDiffSettings	runDiffAnalysis
getDiffSettings,RflomicsMAE-method	runDiffAnalysis
getDiffSettings,RflomicsSE-method	runDiffAnalysis
getDiffStat	runDiffAnalysis
getDiffStat,RflomicsMAE-method	runDiffAnalysis
getDiffStat,RflomicsSE-method	runDiffAnalysis
getEnrichRes	runAnnotationEnrichment
getEnrichRes,RflomicsMAE-method	runAnnotationEnrichment
getEnrichRes,RflomicsSE-method	runAnnotationEnrichment
getEnrichSettings	runAnnotationEnrichment
getEnrichSettings,RflomicsSE-method	runAnnotationEnrichment
getFactorModalities	RflomicsMAE-class
getFactorModalities,RflomicsMAE-method	RflomicsMAE-class
getFactorModalities,RflomicsSE-method	RflomicsSE-class
getFactorNames	RflomicsMAE-class
getFactorNames,RflomicsMAE-method	RflomicsMAE-class
getFactorNames,RflomicsSE-method	RflomicsSE-class
getFactorTypes	RflomicsMAE-class
getFactorTypes,RflomicsMAE-method	RflomicsMAE-class
getFactorTypes,RflomicsSE-method	RflomicsSE-class
getFilteredFeatures	runDataProcessing
getFilteredFeatures,RflomicsMAE-method	runDataProcessing
getFilteredFeatures,RflomicsSE-method	runDataProcessing
getFilterSettings	runDataProcessing
getFilterSettings,RflomicsMAE-method	runDataProcessing
getFilterSettings,RflomicsSE-method	runDataProcessing
getMetaFactors	RflomicsMAE-class
getMetaFactors,RflomicsMAE-method	RflomicsMAE-class
getMetaFactors,RflomicsSE-method	RflomicsSE-class
getMixOmics	runOmicsIntegration
getMixOmics,RflomicsMAE-method	runOmicsIntegration
getMixOmicsSettings	runOmicsIntegration
getMixOmicsSettings,RflomicsMAE-method	runOmicsIntegration
getModelFormula	generateModelFormulae
getModelFormula,RflomicsMAE-method	generateModelFormulae
getModelFormula,RflomicsSE-method	generateModelFormulae
getMOFA	runOmicsIntegration
getMOFA,RflomicsMAE-method	runOmicsIntegration
getMOFASettings	runOmicsIntegration
getMOFASettings,RflomicsMAE-method	runOmicsIntegration
getNormSettings	runDataProcessing
getNormSettings,RflomicsMAE-method	runDataProcessing
getNormSettings,RflomicsSE-method	runDataProcessing
getOmicsTypes	RflomicsMAE-class
getOmicsTypes,RflomicsMAE-method	RflomicsMAE-class
getOmicsTypes,RflomicsSE-method	RflomicsSE-class
getProcessedData	runDataProcessing
getProcessedData,RflomicsMAE-method	runDataProcessing
getProcessedData,RflomicsSE-method	runDataProcessing
getProjectName	RflomicsMAE-class
getProjectName,RflomicsMAE-method	RflomicsMAE-class
getRflomicsSE	RflomicsMAE-class
getRflomicsSE,RflomicsMAE-method	RflomicsMAE-class
getSelectedContrasts	generateExpressionContrast
getSelectedContrasts,RflomicsMAE-method	generateExpressionContrast
getSelectedContrasts,RflomicsSE-method	generateExpressionContrast
getSelectedSamples	runDataProcessing
getSelectedSamples,RflomicsMAE-method	runDataProcessing
getSelectedSamples,RflomicsSE-method	runDataProcessing
getTransSettings	runDataProcessing
getTransSettings,RflomicsMAE-method	runDataProcessing
getTransSettings,RflomicsSE-method	runDataProcessing
getValidContrasts	runDiffAnalysis
getValidContrasts,RflomicsMAE-method	runDiffAnalysis
getValidContrasts,RflomicsSE-method	runDiffAnalysis
isProcessedData	runDataProcessing
isProcessedData,RflomicsMAE-method	runDataProcessing
isProcessedData,RflomicsSE-method	runDataProcessing
plotBoxplotDE	runDiffAnalysis
plotBoxplotDE,RflomicsMAE-method	runDiffAnalysis
plotBoxplotDE,RflomicsSE-method	runDiffAnalysis
plotClusterProfiler	runAnnotationEnrichment
plotClusterProfiler,RflomicsSE-method	runAnnotationEnrichment
plotCoExpression	runCoExpression
plotCoExpression,RflomicsMAE-method	runCoExpression
plotCoExpression,RflomicsSE-method	runCoExpression
plotCoExpressionProfile	runCoExpression
plotCoExpressionProfile,RflomicsMAE-method	runCoExpression
plotCoExpressionProfile,RflomicsSE-method	runCoExpression
plotConditionsOverview	RflomicsMAE-class
plotConditionsOverview,RflomicsMAE-method	RflomicsMAE-class
plotCoseqContrasts	runCoExpression
plotCoseqContrasts,RflomicsMAE-method	runCoExpression
plotCoseqContrasts,RflomicsSE-method	runCoExpression
plotDataDistribution	runDataProcessing
plotDataDistribution,RflomicsMAE-method	runDataProcessing
plotDataDistribution,RflomicsSE-method	runDataProcessing
plotDataOverview	RflomicsMAE-class
plotDataOverview,RflomicsMAE-method	RflomicsMAE-class
plotDiffAnalysis	runDiffAnalysis
plotDiffAnalysis,RflomicsMAE-method	runDiffAnalysis
plotDiffAnalysis,RflomicsSE-method	runDiffAnalysis
plotEnrichComp	runAnnotationEnrichment
plotEnrichComp,RflomicsSE-method	runAnnotationEnrichment
plotExpDesignCompleteness	runDataProcessing
plotExpDesignCompleteness,RflomicsMAE-method	runDataProcessing
plotExpDesignCompleteness,RflomicsSE-method	runDataProcessing
plotHeatmapDesign	runDiffAnalysis
plotHeatmapDesign,RflomicsMAE-method	runDiffAnalysis
plotHeatmapDesign,RflomicsSE-method	runDiffAnalysis
plotLibrarySize	runDataProcessing
plotLibrarySize,RflomicsMAE-method	runDataProcessing
plotLibrarySize,RflomicsSE-method	runDataProcessing
plotOmicsPCA	runDataProcessing
plotOmicsPCA,RflomicsMAE-method	runDataProcessing
plotOmicsPCA,RflomicsSE-method	runDataProcessing
prepareForIntegration	prepareForIntegration
prepareForIntegration,RflomicsMAE-method	prepareForIntegration
RflomicsMAE-class	RflomicsMAE-class
rflomicsMAE2MAE	rflomicsMAE2MAE
rflomicsMAE2MAE,RflomicsMAE-method	rflomicsMAE2MAE
RflomicsSE	RflomicsSE-class
RflomicsSE-class	RflomicsSE-class
runAnnotationEnrichment	runAnnotationEnrichment
runAnnotationEnrichment,RflomicsMAE-method	runAnnotationEnrichment
runAnnotationEnrichment,RflomicsSE-method	runAnnotationEnrichment
runCoExpression	runCoExpression
runCoExpression,RflomicsMAE-method	runCoExpression
runCoExpression,RflomicsSE-method	runCoExpression
runDataProcessing	runDataProcessing
runDataProcessing,RflomicsMAE-method	runDataProcessing
runDataProcessing,RflomicsSE-method	runDataProcessing
runDiffAnalysis	runDiffAnalysis
runDiffAnalysis,RflomicsMAE-method	runDiffAnalysis
runDiffAnalysis,RflomicsSE-method	runDiffAnalysis
runFeatureFiltering	runDataProcessing
runFeatureFiltering,RflomicsMAE-method	runDataProcessing
runFeatureFiltering,RflomicsSE-method	runDataProcessing
runNormalization	runDataProcessing
runNormalization,RflomicsMAE-method	runDataProcessing
runNormalization,RflomicsSE-method	runDataProcessing
runOmicsIntegration	runOmicsIntegration
runOmicsIntegration,RflomicsMAE-method	runOmicsIntegration
runOmicsPCA	runDataProcessing
runOmicsPCA,RflomicsMAE-method	runDataProcessing
runOmicsPCA,RflomicsSE-method	runDataProcessing
runRFLOMICS	runRFLOMICS
runSampleFiltering	runDataProcessing
runSampleFiltering,RflomicsMAE-method	runDataProcessing
runSampleFiltering,RflomicsSE-method	runDataProcessing
runTransformData	runDataProcessing
runTransformData,RflomicsMAE-method	runDataProcessing
runTransformData,RflomicsSE-method	runDataProcessing
setMixOmics	runOmicsIntegration
setMixOmics,RflomicsMAE-method	runOmicsIntegration
setModelFormula	generateModelFormulae
setModelFormula,RflomicsMAE-method	generateModelFormulae
setModelFormula,RflomicsSE-method	generateModelFormulae
setMOFA	runOmicsIntegration
setMOFA,RflomicsMAE-method	runOmicsIntegration
setSelectedContrasts	generateExpressionContrast
setSelectedContrasts,RflomicsMAE-method	generateExpressionContrast
setSelectedContrasts,RflomicsSE-method	generateExpressionContrast
setValidContrasts	runDiffAnalysis
setValidContrasts,RflomicsMAE-method	runDiffAnalysis
setValidContrasts,RflomicsSE-method	runDiffAnalysis
subRflomicsMAE	RflomicsMAE-class
subRflomicsMAE,RflomicsMAE-method	RflomicsMAE-class
sumMixOmics	runOmicsIntegration
sumMixOmics,RflomicsMAE-method	runOmicsIntegration
sumORA	runAnnotationEnrichment
sumORA,RflomicsSE-method	runAnnotationEnrichment
