Interactive web application for Omics-data analysis

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Documentation for package ‘RFLOMICS’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

C E F G I P R S

-- C --

checkExpDesignCompleteness	Data Exploratory and processing
checkExpDesignCompleteness-method	Data Exploratory and processing
createRflomicsMAE	RflomicsMAE class constructor

-- E --

ecoseed.df	Ecoseed project data
ecoseed.mae	Ecoseed project data

-- F --

filterDiffAnalysis	Run Differential Expression Analysis and process results
filterDiffAnalysis-method	Run Differential Expression Analysis and process results

-- G --

generateExpressionContrast	Contrast expressions
generateExpressionContrast-method	Contrast expressions
generateModelFormulae	Statistical model formulae
generateModelFormulae-method	Statistical model formulae
generateReport	Generate RFLOMICS html report or archive
generateReport-method	Generate RFLOMICS html report or archive
getAnalysis	Get results from RFLOMICS object
getAnalysis-method	Get results from RFLOMICS object
getAnalyzedDatasetNames	Get results from RFLOMICS object
getAnalyzedDatasetNames-method	Get results from RFLOMICS object
getAnnotAnalysesSummary	Run Gene Enrichment Analysis and process results
getAnnotAnalysesSummary-method	Run Gene Enrichment Analysis and process results
getBatchFactors	RflomicsMAE Class
getBatchFactors-method	RflomicsMAE Class
getBatchFactors-method	RflomicsSE Class
getBioFactors	RflomicsMAE Class
getBioFactors-method	RflomicsMAE Class
getBioFactors-method	RflomicsSE Class
getCoeffNorm	Data Exploratory and processing
getCoeffNorm-method	Data Exploratory and processing
getCoExpAnalysesSummary	Run CoExpression Analysis and process results
getCoExpAnalysesSummary-method	Run CoExpression Analysis and process results
getCoexpClusters	Run CoExpression Analysis and process results
getCoexpClusters-method	Run CoExpression Analysis and process results
getCoexpSettings	Run CoExpression Analysis and process results
getCoexpSettings-method	Run CoExpression Analysis and process results
getDatasetNames	RflomicsMAE Class
getDatasetNames-method	RflomicsMAE Class
getDatasetNames-method	RflomicsSE Class
getDEList	Run Differential Expression Analysis and process results
getDEList-method	Run Differential Expression Analysis and process results
getDEMatrix	Run Differential Expression Analysis and process results
getDEMatrix-method	Run Differential Expression Analysis and process results
getDesignMat	RflomicsMAE Class
getDesignMat-method	RflomicsMAE Class
getDesignMat-method	RflomicsSE Class
getDiffAnalysesSummary	Run Differential Expression Analysis and process results
getDiffAnalysesSummary-method	Run Differential Expression Analysis and process results
getDiffSettings	Run Differential Expression Analysis and process results
getDiffSettings-method	Run Differential Expression Analysis and process results
getDiffStat	Run Differential Expression Analysis and process results
getDiffStat-method	Run Differential Expression Analysis and process results
getEnrichRes	Run Gene Enrichment Analysis and process results
getEnrichRes-method	Run Gene Enrichment Analysis and process results
getEnrichSettings	Run Gene Enrichment Analysis and process results
getEnrichSettings-method	Run Gene Enrichment Analysis and process results
getFactorModalities	RflomicsMAE Class
getFactorModalities-method	RflomicsMAE Class
getFactorModalities-method	RflomicsSE Class
getFactorNames	RflomicsMAE Class
getFactorNames-method	RflomicsMAE Class
getFactorNames-method	RflomicsSE Class
getFactorTypes	RflomicsMAE Class
getFactorTypes-method	RflomicsMAE Class
getFactorTypes-method	RflomicsSE Class
getFilteredFeatures	Data Exploratory and processing
getFilteredFeatures-method	Data Exploratory and processing
getFilterSettings	Data Exploratory and processing
getFilterSettings-method	Data Exploratory and processing
getMetaFactors	RflomicsMAE Class
getMetaFactors-method	RflomicsMAE Class
getMetaFactors-method	RflomicsSE Class
getMixOmics	runOmicsIntegration
getMixOmics-method	runOmicsIntegration
getMixOmicsSettings	runOmicsIntegration
getMixOmicsSettings-method	runOmicsIntegration
getModelFormula	Statistical model formulae
getModelFormula-method	Statistical model formulae
getMOFA	runOmicsIntegration
getMOFA-method	runOmicsIntegration
getMOFASettings	runOmicsIntegration
getMOFASettings-method	runOmicsIntegration
getNormSettings	Data Exploratory and processing
getNormSettings-method	Data Exploratory and processing
getOmicsTypes	RflomicsMAE Class
getOmicsTypes-method	RflomicsMAE Class
getOmicsTypes-method	RflomicsSE Class
getProcessedData	Data Exploratory and processing
getProcessedData-method	Data Exploratory and processing
getProjectName	RflomicsMAE Class
getProjectName-method	RflomicsMAE Class
getRflomicsSE	RflomicsMAE Class
getRflomicsSE-method	RflomicsMAE Class
getSelectedContrasts	Contrast expressions
getSelectedContrasts-method	Contrast expressions
getSelectedSamples	Data Exploratory and processing
getSelectedSamples-method	Data Exploratory and processing
getTransSettings	Data Exploratory and processing
getTransSettings-method	Data Exploratory and processing
getValidContrasts	Run Differential Expression Analysis and process results
getValidContrasts-method	Run Differential Expression Analysis and process results

-- I --

isProcessedData	Data Exploratory and processing
isProcessedData-method	Data Exploratory and processing

-- P --

plotBoxplotDE	Run Differential Expression Analysis and process results
plotBoxplotDE-method	Run Differential Expression Analysis and process results
plotClusterProfiler	Run Gene Enrichment Analysis and process results
plotClusterProfiler-method	Run Gene Enrichment Analysis and process results
plotCoExpression	Run CoExpression Analysis and process results
plotCoExpression-method	Run CoExpression Analysis and process results
plotCoExpressionProfile	Run CoExpression Analysis and process results
plotCoExpressionProfile-method	Run CoExpression Analysis and process results
plotConditionsOverview	RflomicsMAE Class
plotConditionsOverview-method	RflomicsMAE Class
plotCoseqContrasts	Run CoExpression Analysis and process results
plotCoseqContrasts-method	Run CoExpression Analysis and process results
plotDataDistribution	Data Exploratory and processing
plotDataDistribution-method	Data Exploratory and processing
plotDataOverview	RflomicsMAE Class
plotDataOverview-method	RflomicsMAE Class
plotDiffAnalysis	Run Differential Expression Analysis and process results
plotDiffAnalysis-method	Run Differential Expression Analysis and process results
plotEnrichComp	Run Gene Enrichment Analysis and process results
plotEnrichComp-method	Run Gene Enrichment Analysis and process results
plotExpDesignCompleteness	Data Exploratory and processing
plotExpDesignCompleteness-method	Data Exploratory and processing
plotHeatmapDesign	Run Differential Expression Analysis and process results
plotHeatmapDesign-method	Run Differential Expression Analysis and process results
plotLibrarySize	Data Exploratory and processing
plotLibrarySize-method	Data Exploratory and processing
plotOmicsPCA	Data Exploratory and processing
plotOmicsPCA-method	Data Exploratory and processing
prepareForIntegration	Preparation step for integration
prepareForIntegration-method	Preparation step for integration

-- R --

RflomicsMAE-class	RflomicsMAE Class
rflomicsMAE2MAE	convert a RflomicsMAE to a MultiAssayExperiment
rflomicsMAE2MAE-method	convert a RflomicsMAE to a MultiAssayExperiment
RflomicsSE	RflomicsSE Class
RflomicsSE-class	RflomicsSE Class
runAnnotationEnrichment	Run Gene Enrichment Analysis and process results
runAnnotationEnrichment-method	Run Gene Enrichment Analysis and process results
runCoExpression	Run CoExpression Analysis and process results
runCoExpression-method	Run CoExpression Analysis and process results
runDataProcessing	Data Exploratory and processing
runDataProcessing-method	Data Exploratory and processing
runDiffAnalysis	Run Differential Expression Analysis and process results
runDiffAnalysis-method	Run Differential Expression Analysis and process results
runFeatureFiltering	Data Exploratory and processing
runFeatureFiltering-method	Data Exploratory and processing
runNormalization	Data Exploratory and processing
runNormalization-method	Data Exploratory and processing
runOmicsIntegration	runOmicsIntegration
runOmicsIntegration-method	runOmicsIntegration
runOmicsPCA	Data Exploratory and processing
runOmicsPCA-method	Data Exploratory and processing
runRFLOMICS	Run RFLOMICS interface
runSampleFiltering	Data Exploratory and processing
runSampleFiltering-method	Data Exploratory and processing
runTransformData	Data Exploratory and processing
runTransformData-method	Data Exploratory and processing

-- S --

setMixOmics	runOmicsIntegration
setMixOmics-method	runOmicsIntegration
setModelFormula	Statistical model formulae
setModelFormula-method	Statistical model formulae
setMOFA	runOmicsIntegration
setMOFA-method	runOmicsIntegration
setSelectedContrasts	Contrast expressions
setSelectedContrasts-method	Contrast expressions
setValidContrasts	Run Differential Expression Analysis and process results
setValidContrasts-method	Run Differential Expression Analysis and process results
subRflomicsMAE	RflomicsMAE Class
subRflomicsMAE-method	RflomicsMAE Class
sumMixOmics	runOmicsIntegration
sumMixOmics-method	runOmicsIntegration
sumORA	Run Gene Enrichment Analysis and process results
sumORA-method	Run Gene Enrichment Analysis and process results