Integrate microRNA and gene expression to decipher pathway complexity

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Documentation for package ‘MIRit’ version 1.5.2

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

Help Pages

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