addDifferentialExpression
                        Manually add differential expression results to
                        a MirnaExperiment object
augmentedPathways       Access the miRNA-augmented pathways that were
                        used during TAIPA
batchCorrection         Correct for batch effects in miRNA and gene
                        expression measurements
deAccessors             Extract differentially expressed miRNAs and
                        genes from a 'MirnaExperiment' object
deAnalysis              Perform differential expression analysis
enrichedFeatures        Extract the names of the pre-ranked features in
                        a GSEA experiment
enrichGenes             Perform functional enrichment analysis of genes
enrichmentBarplot       Create a barplot for functional enrichment
                        analysis
enrichmentDatabase      Access the database used for functional
                        enrichment analyses
enrichmentDotplot       Create a dotplot for functional enrichment
                        analysis
enrichmentMethod        Access the method used for functional
                        enrichment analyses
enrichmentMetric        Extract the GSEA ranking metric used for
                        functional enrichment analyses
enrichmentResults       Access the results of functional enrichment
                        analyses
enrichTargets           Perform an enrichment analysis of integrated
                        microRNA targets
findMirnaSNPs           Find disease-associated SNPs occurring at
                        DE-miRNA loci
FunctionalEnrichment-class
                        The 'FunctionalEnrichment' class
geneCounts              Count matrix for gene expression in thyroid
                        cancer
geneSet                 Extract the gene-sets used for functional
                        enrichment analyses
getEvidence             Get the scientific evidence for a particular
                        disease-SNP association
getTargets              Get microRNA targets
gseaPlot                Create a GSEA plot that displays the running
                        enrichment score (ES) for a given pathway
gseaRidgeplot           Create a ridgeplot to display the results of
                        GSEA analysis
integratedPathways      Access the results of integrative miRNA-mRNA
                        pathway analyses
integration             Explore the results of the integration analysis
                        between miRNAs and genes
integrationDatabase     Extract the database used for integrative
                        miRNA-mRNA pathway analyses
integrationDotplot      Display integrated miRNA-mRNA augmented
                        pathways in a dotplot
IntegrativePathwayAnalysis-class
                        The 'IntegrativePathwayAnalysis' class
listPathways            List all the available biological pathways in
                        KEGG, Reactome and WikiPathways
loadExamples            Load example MIRit objects
mirnaCounts             Count matrix for microRNA expression in thyroid
                        cancer
MirnaExperiment         The constructor function for MirnaExperiment
MirnaExperiment-class   The 'MirnaExperiment' class
mirnaIntegration        Integrate microRNA and gene expression
mirnaTargets            Explore miRNA-target pairs
mirVariantPlot          Create a trackplot to show the association
                        between miRNAs and disease-SNPs
pairedSamples           View the relationship between miRNA and gene
                        samples
plotCorrelation         Plot correlation between miRNAs and genes
                        within biological groups
plotDE                  Represent differentially expressed miRNAs/genes
                        as boxplots, barplots or violinplots
plotDimensions          Generate multidimensional scaling (MDS) plots
                        to explore miRNA/gene expression distances
plotVolcano             Produce volcano plots to display miRNA/gene
                        differential expression
preparePathways         Prepare miRNA-augmented pathways for
                        integrative miRNA-mRNA pathway analyses
searchDisease           Search for disease EFO identifiers
setTargets              Use custom miRNA-target interactions
significantAccessors    Get the IDs of statistically differentially
                        expressed miRNAs/genes
supportedOrganisms      Get the list of supported organisms for a given
                        database
topologicalAnalysis     Perform a topologically-aware integrative
                        pathway analysis (TAIPA)
visualizeNetwork        Visualize the relationships between miRNAs and
                        genes in a biological pathway
