Package: miREA 0.99.2

Zhesi Zhang

miREA: Network-Based Edge-Centric MicroRNA-Oriented Enrichment Analysis

miREA performs microRNA-oriented enrichment analysis by modeling miRNA-gene interaction (MGI) networks directly, rather than collapsing them to miRNA- or gene-level sets. It implements four node-based methods and five edge-based methods spanning over-representation, scoring-based, topology-aware, and network-propagation approaches, using expression-informed MGI edge scores to characterize regulatory strength. The package also provides heatmap, Sankey, and summary visualizations to explore miRNA-gene-pathway regulatory mechanisms discovered by the enrichment results.

Authors:Zhesi Zhang [aut, cre], Xin Lai [aut], Tampere University [fnd]

miREA_0.99.2.tar.gz
miREA_0.99.2.zip(r-4.7-any)miREA_0.99.2.zip(r-4.6-any)miREA_0.99.2.zip(r-4.5-any)
miREA_0.99.2.tgz(r-4.6-any)miREA_0.99.2.tgz(r-4.5-any)
miREA_0.99.2.tar.gz(r-4.7-any)miREA_0.99.2.tar.gz(r-4.6-any)
miREA_0.99.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
miREA/json (API)

# Install 'miREA' in R:

install.packages('miREA', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/laixn/mirea/issues

Datasets:

toy_background_GGI - Toy BLCA example data for miREA
toy_background_MGI - Toy BLCA example data for miREA
toy_gene_DEdata - Toy BLCA example data for miREA
toy_gene_mat - Toy BLCA example data for miREA
toy_mir_DEdata - Toy BLCA example data for miREA
toy_mir_mat - Toy BLCA example data for miREA
toy_pathway - Toy BLCA example data for miREA

On CRAN:

mirna geneexpression genesetenrichment network networkenrichment pathways systemsbiology

2.70 score 24 exports 139 dependencies

Last updated from:04147f8382. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	197
linux-devel	OK	669
source / vignettes	OK	371
linux-release	OK	715
macos-release	OK	708
macos-oldrel	OK	754
windows-devel	OK	671
windows-release	OK	651
windows-oldrel	OK	585
wasm-release	OK	153

Exports:as.data.frame default_GGI_source default_method_list default_pAdjMethod default_pathway_list default_pvalueType default_scoreFun default_TP_cancer Edge_Network Edge_ORA Edge_Score1D Edge_Score2D Edge_Topology getAllInputData MiR_ORA MiR_Score miREA miREAResult plotHeatmap plotHeatmapSankey plotSummary show TG_ORA TG_Score

Dependencies:aisdk AnnotationDbi ape aplot askpass base64enc Biobase BiocBaseUtils BiocGenerics Biostrings bit bit64 blob bslib cachem callr circlize cli clue cluster clusterProfiler codetools colorspace ComplexHeatmap cpp11 crayon curl data.table DBI digest doParallel DOSE dplyr enrichit enrichplot evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver foreach fs gdtools generics GetoptLong ggalluvial ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggrepel ggtangle ggtree GlobalOptions glue GO.db GOSemSim gridGraphics gson gtable highr htmltools htmlwidgets httr httr2 igraph IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lattice lazyeval lifecycle magrittr MASS Matrix matrixStats memoise mime miRBaseConverter nlme openssl otel patchwork pillar pkgconfig plyr png polyclip processx ps purrr qvalue R6 rappdirs RColorBrewer Rcpp RcppEigen reshape2 RhpcBLASctl rjson rlang rmarkdown RSQLite S4Vectors S7 sass scales scatterpie Seqinfo shape stringi stringr sys systemfonts tibble tidydr tidyr tidyselect tidytree tinytex treeio tweenr utf8 vctrs viridisLite withr xfun XVector yaml yulab.utils

Quick Start: miRNA-oriented enrichment analysis with miREA

Rendered frommiREA.Rmdusingknitr::rmarkdown

Last update: 2026-10-15
Started: 2026-10-12

Help page	Topics
Supported gene-gene interaction sources	default_GGI_source
Supported enrichment methods	default_method_list
Supported p-value adjustment methods	default_pAdjMethod
Supported predefined pathway sets	default_pathway_list
Supported GSEA score types	default_pvalueType
Supported score transformations	default_scoreFun
Cancer types used for the TP pathway set	default_TP_cancer
Edge-Network (MGI Edge Network Enrichment Analysis)	Edge_Network
Edge-ORA (MiRNA-Gene Interaction Edge Over-Representation Analysis)	Edge_ORA
Edge-Score1D (MiRNA-Gene Interaction Edge Score-based Analysis)	Edge_Score1D
Edge-Score2D (MiRNA-Gene Interaction 2D Edge Score-based Analysis)	Edge_Score2D
Edge-Topology (MGI Edge Pathway Topology Enrichment Analysis)	Edge_Topology
Generate input data for miREA	getAllInputData
MiR-ORA (MiRNA Over-Representation Analysis)	MiR_ORA
MiR-Score (MiRNA Score-based Analysis)	MiR_Score
MGI edge-based microRNA-oriented enrichment analysis	miREA
Toy BLCA example data for miREA	miREA_example_data toy_background_GGI toy_background_MGI toy_gene_DEdata toy_gene_mat toy_mir_DEdata toy_mir_mat toy_pathway
S4 class for miREA() results	$,miREAResult-method as.data.frame,miREAResult-method miREAResult miREAResult-class show,miREAResult-method [[,miREAResult-method
Visualize an enrichment result as a heatmap	plotHeatmap
Visualize an enrichment result as a combined heatmap-Sankey plot	plotHeatmapSankey
Visualize and compare enrichment results across methods	plotSummary
TG-ORA (Target Gene Over-Representation Analysis)	TG_ORA
TG-Score (Target Gene Score-based Analysis)	TG_Score

Package: miREA 0.99.2

miREA: Network-Based Edge-Centric MicroRNA-Oriented Enrichment Analysis

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Help Manual

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