MIRit-package	MIRit-package
addDifferentialExpression	addDifferentialExpression
augmentedPathways	augmentedPathways
augmentedPathways,IntegrativePathwayAnalysis-method	IntegrativePathwayAnalysis-class
batchCorrection	batchCorrection
deAccessors	deAccessors
deAnalysis	deAnalysis
enrichedFeatures	enrichedFeatures
enrichedFeatures,FunctionalEnrichment-method	FunctionalEnrichment-class
enrichGenes	enrichGenes
enrichmentBarplot	enrichmentBarplot
enrichmentDatabase	enrichmentDatabase
enrichmentDatabase,FunctionalEnrichment-method	FunctionalEnrichment-class
enrichmentDotplot	enrichmentDotplot
enrichmentMethod	enrichmentMethod
enrichmentMethod,FunctionalEnrichment-method	FunctionalEnrichment-class
enrichmentMetric	enrichmentMetric
enrichmentMetric,FunctionalEnrichment-method	FunctionalEnrichment-class
enrichmentResults	enrichmentResults
enrichmentResults,FunctionalEnrichment-method	FunctionalEnrichment-class
enrichTargets	enrichTargets
findMirnaSNPs	findMirnaSNPs
FunctionalEnrichment	FunctionalEnrichment-class
FunctionalEnrichment-class	FunctionalEnrichment-class
geneCounts	geneCounts
geneDE	deAccessors
geneDE,MirnaExperiment-method	MirnaExperiment-class
geneSet	geneSet
geneSet,FunctionalEnrichment-method	FunctionalEnrichment-class
getEvidence	getEvidence
getTargets	getTargets
gseaPlot	gseaPlot
gseaRidgeplot	gseaRidgeplot
integratedPathways	integratedPathways
integratedPathways,IntegrativePathwayAnalysis-method	IntegrativePathwayAnalysis-class
integration	integration
integration,MirnaExperiment-method	MirnaExperiment-class
integrationDatabase	integrationDatabase
integrationDatabase,IntegrativePathwayAnalysis-method	IntegrativePathwayAnalysis-class
integrationDotplot	integrationDotplot
IntegrativePathwayAnalysis	IntegrativePathwayAnalysis-class
IntegrativePathwayAnalysis-class	IntegrativePathwayAnalysis-class
listPathways	listPathways
loadExamples	loadExamples
MIRit	MIRit-package
mirnaCounts	mirnaCounts
mirnaDE	deAccessors
mirnaDE,MirnaExperiment-method	MirnaExperiment-class
MirnaExperiment	MirnaExperiment
MirnaExperiment-class	MirnaExperiment-class
mirnaIntegration	mirnaIntegration
mirnaTargets	mirnaTargets
mirnaTargets,MirnaExperiment-method	MirnaExperiment-class
mirVariantPlot	mirVariantPlot
pairedSamples	pairedSamples
pairedSamples,MirnaExperiment-method	MirnaExperiment-class
performGeneDE	deAnalysis
performMirnaDE	deAnalysis
plotCorrelation	plotCorrelation
plotDE	plotDE
plotDimensions	plotDimensions
plotVolcano	plotVolcano
preparePathways	preparePathways
searchDisease	searchDisease
show,FunctionalEnrichment-method	FunctionalEnrichment-class
show,IntegrativePathwayAnalysis-method	IntegrativePathwayAnalysis-class
show,MirnaExperiment-method	MirnaExperiment-class
significantAccessors	significantAccessors
significantGenes	significantAccessors
significantGenes,MirnaExperiment-method	MirnaExperiment-class
significantMirnas	significantAccessors
significantMirnas,MirnaExperiment-method	MirnaExperiment-class
supportedOrganisms	supportedOrganisms
topologicalAnalysis	topologicalAnalysis
visualizeNetwork	visualizeNetwork
