Package: MIRit 1.3.0

Jacopo Ronchi

MIRit: Integrate microRNA and gene expression to decipher pathway complexity

MIRit is an R package that provides several methods for investigating the relationships between miRNAs and genes in different biological conditions. In particular, MIRit allows to explore the functions of dysregulated miRNAs, and makes it possible to identify miRNA-gene regulatory axes that control biological pathways, thus enabling the users to unveil the complexity of miRNA biology. MIRit is an all-in-one framework that aims to help researchers in all the central aspects of an integrative miRNA-mRNA analyses, from differential expression analysis to network characterization.

Authors:Jacopo Ronchi [aut, cre], Maria Foti [fnd]

MIRit_1.3.0.tar.gz
MIRit_1.3.0.zip(r-4.5)MIRit_1.3.0.zip(r-4.4)MIRit_1.1.0.zip(r-4.3)
MIRit_1.3.0.tgz(r-4.4-x86_64)MIRit_1.3.0.tgz(r-4.4-arm64)MIRit_1.1.0.tgz(r-4.3-x86_64)MIRit_1.1.0.tgz(r-4.3-arm64)
MIRit_1.3.0.tar.gz(r-4.5-noble)MIRit_1.3.0.tar.gz(r-4.4-noble)
MIRit_1.3.0.tgz(r-4.4-emscripten)MIRit_1.1.0.tgz(r-4.3-emscripten)
MIRit.pdf |MIRit.html✨
MIRit/json (API)
NEWS

# Install 'MIRit' in R:
install.packages('MIRit', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jacopo-ronchi/mirit/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • geneCounts - Count matrix for gene expression in thyroid cancer
  • mirnaCounts - Count matrix for microRNA expression in thyroid cancer

On BioConductor:MIRit-1.3.0(bioc 3.21)MIRit-1.2.0(bioc 3.20)

softwaregeneregulationnetworkenrichmentnetworkinferenceepigeneticsfunctionalgenomicssystemsbiologynetworkpathwaysgeneexpressiondifferentialexpressionmirnamirna-mrna-interactionmirna-seqmirnaseq-analysiscpp

4.48 score 2 scripts 140 downloads 45 exports 184 dependencies

Last updated 2 months agofrom:57bfd48593. Checks:OK: 1 ERROR: 6 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 17 2024
R-4.5-win-x86_64ERRORDec 17 2024
R-4.5-linux-x86_64ERRORDec 17 2024
R-4.4-win-x86_64ERRORDec 17 2024
R-4.4-mac-x86_64NOTEDec 17 2024
R-4.4-mac-aarch64NOTEDec 17 2024
R-4.3-win-x86_64ERRORSep 26 2024
R-4.3-mac-x86_64ERRORSep 26 2024
R-4.3-mac-aarch64ERRORSep 26 2024

Exports:addDifferentialExpressionaugmentedPathwaysbatchCorrectionenrichedFeaturesenrichGenesenrichmentBarplotenrichmentDatabaseenrichmentDotplotenrichmentMethodenrichmentMetricenrichmentResultsenrichTargetsfindMirnaSNPsgeneDEgeneSetgetEvidencegetTargetsgseaPlotgseaRidgeplotintegratedPathwaysintegrationintegrationDatabaseintegrationDotplotlistPathwaysloadExamplesmirnaDEMirnaExperimentmirnaIntegrationmirnaTargetsmirVariantPlotpairedSamplesperformGeneDEperformMirnaDEplotCorrelationplotDEplotDimensionsplotVolcanopreparePathwayssearchDiseaseshowsignificantGenessignificantMirnassupportedOrganismstopologicalAnalysisvisualizeNetwork

Dependencies:abindAnnotationDbiapeaplotaskpassbackportsBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocParallelBiostringsbitbit64bitopsblobbootbroomcachemcarcarDatacliclusterProfilercodetoolscolorspacecorrplotcowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDerivDESeq2digestdoByDOSEdplyredgeRenrichploteuropepmcfansifarverfastmapfastmatchfgseafilelockformatRFormulafsfstfstcorefutile.loggerfutile.optionsgenekitrgenericsgenesetGenomeInfoDbGenomeInfoDbDataGenomicRangesggforceggfunggnewscaleggplot2ggplotifyggpubrggraphggrepelggsciggsignifggtangleggtreeggvennglueGO.dbGOSemSimgraphgraphitegraphlayoutsgridExtragridGraphicsgsongtablehmshttrigraphIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclelimmalme4locfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrMultiAssayExperimentmunsellnlmenloptrnnetnumDerivopensslopenxlsxpatchworkpbkrtestpillarpkgconfigplogrplyrpngpolyclippolynomprettyunitsprogresspurrrquantregqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreshape2RgraphvizrlangRSQLiterstatixS4ArraysS4VectorsscalesscatterpiesnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstibbletidygraphtidyrtidyselecttidytreetreeiotriebeardtweenrUCSC.utilsurltoolsutf8vctrsviridisviridisLitewithrxml2XVectoryulab.utilszipzlibbioc

Integrate miRNA and gene expression data with MIRit

Jacopo Ronchi

Rendered fromMIRit.Rmdusingknitr::rmarkdownon Dec 17 2024.

Last update: 2024-10-23
Started: 2023-02-19

Readme and manuals

Help Manual

Help pageTopics
Manually add differential expression results to a MirnaExperiment objectaddDifferentialExpression
Access the miRNA-augmented pathways that were used during TAIPAaugmentedPathways
Correct for batch effects in miRNA and gene expression measurementsbatchCorrection
Extract differentially expressed miRNAs and genes from a 'MirnaExperiment' objectdeAccessors geneDE mirnaDE
Perform differential expression analysisdeAnalysis performGeneDE performMirnaDE
Extract the names of the pre-ranked features in a GSEA experimentenrichedFeatures
Perform functional enrichment analysis of genesenrichGenes
Create a barplot for functional enrichment analysisenrichmentBarplot
Access the database used for functional enrichment analysesenrichmentDatabase
Create a dotplot for functional enrichment analysisenrichmentDotplot
Access the method used for functional enrichment analysesenrichmentMethod
Extract the GSEA ranking metric used for functional enrichment analysesenrichmentMetric
Access the results of functional enrichment analysesenrichmentResults
Perform an enrichment analysis of integrated microRNA targetsenrichTargets
Find disease-associated SNPs occurring at DE-miRNA locifindMirnaSNPs
The 'FunctionalEnrichment' classenrichedFeatures,FunctionalEnrichment-method enrichmentDatabase,FunctionalEnrichment-method enrichmentMethod,FunctionalEnrichment-method enrichmentMetric,FunctionalEnrichment-method enrichmentResults,FunctionalEnrichment-method FunctionalEnrichment FunctionalEnrichment-class geneSet,FunctionalEnrichment-method show,FunctionalEnrichment-method
Count matrix for gene expression in thyroid cancergeneCounts
Extract the gene-sets used for functional enrichment analysesgeneSet
Get the scientific evidence for a particular disease-SNP associationgetEvidence
Get microRNA targetsgetTargets
Create a GSEA plot that displays the running enrichment score (ES) for a given pathwaygseaPlot
Create a ridgeplot to display the results of GSEA analysisgseaRidgeplot
Access the results of integrative miRNA-mRNA pathway analysesintegratedPathways
Explore the results of the integration analysis between miRNAs and genesintegration
Extract the database used for integrative miRNA-mRNA pathway analysesintegrationDatabase
Display integrated miRNA-mRNA augmented pathways in a dotplotintegrationDotplot
The 'IntegrativePathwayAnalysis' classaugmentedPathways,IntegrativePathwayAnalysis-method integratedPathways,IntegrativePathwayAnalysis-method integrationDatabase,IntegrativePathwayAnalysis-method IntegrativePathwayAnalysis IntegrativePathwayAnalysis-class show,IntegrativePathwayAnalysis-method
List all the available biological pathways in KEGG, Reactome and WikiPathwayslistPathways
Load example MIRit objectsloadExamples
Count matrix for microRNA expression in thyroid cancermirnaCounts
The constructor function for MirnaExperimentMirnaExperiment
The 'MirnaExperiment' classgeneDE,MirnaExperiment-method integration,MirnaExperiment-method mirnaDE,MirnaExperiment-method MirnaExperiment-class mirnaTargets,MirnaExperiment-method pairedSamples,MirnaExperiment-method show,MirnaExperiment-method significantGenes,MirnaExperiment-method significantMirnas,MirnaExperiment-method
Integrate microRNA and gene expressionmirnaIntegration
Explore miRNA-target pairsmirnaTargets
Create a trackplot to show the association between miRNAs and disease-SNPsmirVariantPlot
View the relationship between miRNA and gene samplespairedSamples
Plot correlation between miRNAs and genes within biological groupsplotCorrelation
Represent differentially expressed miRNAs/genes as boxplots, barplots or violinplotsplotDE
Generate multidimensional scaling (MDS) plots to explore miRNA/gene expression distancesplotDimensions
Produce volcano plots to display miRNA/gene differential expressionplotVolcano
Prepare miRNA-augmented pathways for integrative miRNA-mRNA pathway analysespreparePathways
Search for disease EFO identifierssearchDisease
Get the IDs of statistically differentially expressed miRNAs/genessignificantAccessors significantGenes significantMirnas
Get the list of supported organisms for a given databasesupportedOrganisms
Perform a topologically-aware integrative pathway analysis (TAIPA)topologicalAnalysis
Visualize the relationships between miRNAs and genes in a biological pathwayvisualizeNetwork