Package: MIRit 1.1.0

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_1.1.0.tar.gz
MIRit_1.1.0.zip(r-4.5)MIRit_1.1.0.zip(r-4.4)MIRit_1.1.0.zip(r-4.3)
MIRit_1.1.0.tgz(r-4.4-arm64)MIRit_1.1.0.tgz(r-4.4-x86_64)MIRit_1.1.0.tgz(r-4.3-arm64)MIRit_1.1.0.tgz(r-4.3-x86_64)
MIRit_1.1.0.tar.gz(r-4.5-noble)MIRit_1.1.0.tar.gz(r-4.4-noble)
MIRit_1.1.0.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'))

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-1.1.0(bioc 3.20)MIRit-1.0.0(bioc 3.19)

bioconductor-package

45 exports 2.09 score 185 dependencies

Last updated 2 months agofrom:3abb82162a

Exports:addDifferentialExpression augmentedPathways batchCorrection enrichedFeatures enrichGenes enrichmentBarplot enrichmentDatabase enrichmentDotplot enrichmentMethod enrichmentMetric enrichmentResults enrichTargets findMirnaSNPs geneDE geneSet getEvidence getTargets gseaPlot gseaRidgeplot integratedPathways integration integrationDatabase integrationDotplot listPathways loadExamples mirnaDE MirnaExperiment mirnaIntegration mirnaTargets mirVariantPlot pairedSamples performGeneDE performMirnaDE plotCorrelation plotDE plotDimensions plotVolcano preparePathways searchDisease show significantGenes significantMirnas supportedOrganisms topologicalAnalysis visualizeNetwork

Dependencies:abind AnnotationDbi ape aplot askpass backports BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocParallel Biostrings bit bit64 bitops blob boot broom cachem car carData cellranger cli clusterProfiler codetools colorspace corrplot cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray Deriv DESeq2 digest doBy DOSE downloader dplyr edgeR enrichplot europepmc fansi farver fastmap fastmatch fgsea filelock formatR fs fst fstcore futile.logger futile.options genekitr generics geneset GenomeInfoDb GenomeInfoDbData GenomicRanges ggforce ggfun ggnewscale ggplot2 ggplotify ggpubr ggraph ggrepel ggsci ggsignif ggtree ggvenn glue GO.db GOSemSim graph graphite graphlayouts gridExtra gridGraphics gson gtable HDO.db hms httr igraph IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lazyeval lifecycle limma lme4 locfit magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv microbenchmark mime minqa modelr MultiAssayExperiment munsell nlme nloptr nnet numDeriv openssl openxlsx patchwork pbkrtest pillar pkgconfig plogr plyr png polyclip polynom prettyunits progress purrr quantreg qvalue R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl readxl rematch reshape2 Rgraphviz rlang RSQLite rstatix S4Arrays S4Vectors scales scatterpie shadowtext snow SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys systemfonts tibble tidygraph tidyr tidyselect tidytree treeio triebeard tweenr UCSC.utils urltools utf8 vctrs viridis viridisLite withr xml2 XVector yulab.utils zip zlibbioc

Integrate miRNA and gene expression data with MIRit

Jacopo Ronchi

Rendered fromMIRit.Rmdusingknitr::rmarkdownon Jun 27 2024.

Last update: 2024-02-12
Started: 2023-02-19

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

Package: MIRit 1.1.0

MIRit: Integrate microRNA and gene expression to decipher pathway complexity

Integrate miRNA and gene expression data with MIRit

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)