addDifferentialExpression | Manually add differential expression results to a MirnaExperiment object |
augmentedPathways | Access the miRNA-augmented pathways that were used during TAIPA |
augmentedPathways-method | The 'IntegrativePathwayAnalysis' class |
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 |
enrichedFeatures-method | The 'FunctionalEnrichment' class |
enrichGenes | Perform functional enrichment analysis of genes |
enrichmentBarplot | Create a barplot for functional enrichment analysis |
enrichmentDatabase | Access the database used for functional enrichment analyses |
enrichmentDatabase-method | The 'FunctionalEnrichment' class |
enrichmentDotplot | Create a dotplot for functional enrichment analysis |
enrichmentMethod | Access the method used for functional enrichment analyses |
enrichmentMethod-method | The 'FunctionalEnrichment' class |
enrichmentMetric | Extract the GSEA ranking metric used for functional enrichment analyses |
enrichmentMetric-method | The 'FunctionalEnrichment' class |
enrichmentResults | Access the results of functional enrichment analyses |
enrichmentResults-method | The 'FunctionalEnrichment' class |
enrichTargets | Perform an enrichment analysis of integrated microRNA targets |
findMirnaSNPs | Find disease-associated SNPs occurring at DE-miRNA loci |
FunctionalEnrichment | The 'FunctionalEnrichment' class |
FunctionalEnrichment-class | The 'FunctionalEnrichment' class |
geneCounts | Count matrix for gene expression in thyroid cancer |
geneDE | Extract differentially expressed miRNAs and genes from a 'MirnaExperiment' object |
geneDE-method | The 'MirnaExperiment' class |
geneSet | Extract the gene-sets used for functional enrichment analyses |
geneSet-method | The 'FunctionalEnrichment' class |
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 |
integratedPathways-method | The 'IntegrativePathwayAnalysis' class |
integration | Explore the results of the integration analysis between miRNAs and genes |
integration-method | The 'MirnaExperiment' class |
integrationDatabase | Extract the database used for integrative miRNA-mRNA pathway analyses |
integrationDatabase-method | The 'IntegrativePathwayAnalysis' class |
integrationDotplot | Display integrated miRNA-mRNA augmented pathways in a dotplot |
IntegrativePathwayAnalysis | The 'IntegrativePathwayAnalysis' class |
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 |
mirnaDE | Extract differentially expressed miRNAs and genes from a 'MirnaExperiment' object |
mirnaDE-method | The 'MirnaExperiment' class |
MirnaExperiment | The constructor function for MirnaExperiment |
MirnaExperiment-class | The 'MirnaExperiment' class |
mirnaIntegration | Integrate microRNA and gene expression |
mirnaTargets | Explore miRNA-target pairs |
mirnaTargets-method | The 'MirnaExperiment' class |
mirVariantPlot | Create a trackplot to show the association between miRNAs and disease-SNPs |
pairedSamples | View the relationship between miRNA and gene samples |
pairedSamples-method | The 'MirnaExperiment' class |
performGeneDE | Perform differential expression analysis |
performMirnaDE | Perform differential expression analysis |
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 |
show-method | The 'FunctionalEnrichment' class |
show-method | The 'IntegrativePathwayAnalysis' class |
show-method | The 'MirnaExperiment' class |
significantAccessors | Get the IDs of statistically differentially expressed miRNAs/genes |
significantGenes | Get the IDs of statistically differentially expressed miRNAs/genes |
significantGenes-method | The 'MirnaExperiment' class |
significantMirnas | Get the IDs of statistically differentially expressed miRNAs/genes |
significantMirnas-method | The 'MirnaExperiment' class |
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 |