# Interactive web application for Omics-data analysis

## Documentation for package ‘RFLOMICS’ version 1.4.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

C E F G I P R S

## -- C --

checkExpDesignCompleteness | Omic Data Exploratory and Preprocessing
checkExpDesignCompleteness-method | Omic Data Exploratory and Preprocessing
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 | Omic Data Exploratory and Preprocessing
getCoeffNorm-method | Omic Data Exploratory and Preprocessing
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 | Omic Data Exploratory and Preprocessing
getFilteredFeatures-method | Omic Data Exploratory and Preprocessing
getFilterSettings | Omic Data Exploratory and Preprocessing
getFilterSettings-method | Omic Data Exploratory and Preprocessing
getImputSettings | Omic Data Exploratory and Preprocessing
getImputSettings-method | Omic Data Exploratory and Preprocessing
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 | Omic Data Exploratory and Preprocessing
getNormSettings-method | Omic Data Exploratory and Preprocessing
getOmicsTypes | RflomicsMAE Class
getOmicsTypes-method | RflomicsMAE Class
getOmicsTypes-method | RflomicsSE Class
getProcessedData | Omic Data Exploratory and Preprocessing
getProcessedData-method | Omic Data Exploratory and Preprocessing
getProjectName | RflomicsMAE Class
getProjectName-method | RflomicsMAE Class
getRflomicsSE | RflomicsMAE Class
getRflomicsSE-method | RflomicsMAE Class
getSelectedContrasts | Contrast expressions
getSelectedContrasts-method | Contrast expressions
getSelectedSamples | Omic Data Exploratory and Preprocessing
getSelectedSamples-method | Omic Data Exploratory and Preprocessing
getTransSettings | Omic Data Exploratory and Preprocessing
getTransSettings-method | Omic Data Exploratory and Preprocessing
getValidContrasts | Run Differential Expression Analysis and process results
getValidContrasts-method | Run Differential Expression Analysis and process results

## -- I --

isProcessedData | Omic Data Exploratory and Preprocessing
isProcessedData-method | Omic Data Exploratory and Preprocessing

## -- 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 | Omic Data Exploratory and Preprocessing
plotDataDistribution-method | Omic Data Exploratory and Preprocessing
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 | Omic Data Exploratory and Preprocessing
plotExpDesignCompleteness-method | Omic Data Exploratory and Preprocessing
plotHeatmapDesign | Run Differential Expression Analysis and process results
plotHeatmapDesign-method | Run Differential Expression Analysis and process results
plotLibrarySize | Omic Data Exploratory and Preprocessing
plotLibrarySize-method | Omic Data Exploratory and Preprocessing
plotMissingValues | Omic Data Exploratory and Preprocessing
plotMissingValues-method | Omic Data Exploratory and Preprocessing
plotOmicsPCA | Omic Data Exploratory and Preprocessing
plotOmicsPCA-method | Omic Data Exploratory and Preprocessing
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 | Omic Data Exploratory and Preprocessing
runDataProcessing-method | Omic Data Exploratory and Preprocessing
runDiffAnalysis | Run Differential Expression Analysis and process results
runDiffAnalysis-method | Run Differential Expression Analysis and process results
runFeatureFiltering | Omic Data Exploratory and Preprocessing
runFeatureFiltering-method | Omic Data Exploratory and Preprocessing
runMVImputation | Omic Data Exploratory and Preprocessing
runMVImputation-method | Omic Data Exploratory and Preprocessing
runNormalization | Omic Data Exploratory and Preprocessing
runNormalization-method | Omic Data Exploratory and Preprocessing
runOmicsIntegration | runOmicsIntegration
runOmicsIntegration-method | runOmicsIntegration
runOmicsPCA | Omic Data Exploratory and Preprocessing
runOmicsPCA-method | Omic Data Exploratory and Preprocessing
runRFLOMICS | Run RFLOMICS interface
runSampleFiltering | Omic Data Exploratory and Preprocessing
runSampleFiltering-method | Omic Data Exploratory and Preprocessing
runTransformData | Omic Data Exploratory and Preprocessing
runTransformData-method | Omic Data Exploratory and Preprocessing

## -- 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