Package: miREA
Title: Network-Based Edge-Centric MicroRNA-Oriented Enrichment Analysis
Version: 0.99.2
Authors@R: c(
    person("Zhesi", "Zhang", role = c("aut", "cre"),
           email = "zhesizhang07@gmail.com",
           comment = c(ORCID = "0009-0006-9869-9455")),
    person("Xin", "Lai", role = "aut",
           comment = c(ORCID = "0000-0003-4913-5822")),
    person("Tampere University", role = "fnd",
           comment = "PROFI6 Health Data Science program"))
Description: 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.
License: Artistic-2.0
URL: https://github.com/laixn/miREA
BugReports: https://github.com/laixn/miREA/issues
biocViews: miRNA, GeneExpression, GeneSetEnrichment, Network,
        NetworkEnrichment, Pathways, SystemsBiology
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = FALSE)
Depends: R (>= 4.5.0)
Imports: BiocGenerics, ComplexHeatmap, circlize, clusterProfiler,
        data.table, dplyr, ggalluvial, ggnewscale, ggplot2, grDevices,
        graphics, grid, igraph, Matrix, methods, miRBaseConverter,
        parallel, patchwork, reshape2, RhpcBLASctl, scales, stats,
        tibble, utils, withr
Suggests: BiocStyle, GSEABase, knitr, rmarkdown, SummarizedExperiment,
        testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev perl zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-16 18:34:01 UTC
RemoteUrl: https://github.com/BiocStaging/miREA
RemoteRef: HEAD
RemoteSha: 04147f83822ac5d6acb9ae7f559500f319ba0e3e
NeedsCompilation: no
Packaged: 2026-10-16 21:32:36 UTC; root
Author: Zhesi Zhang [aut, cre] (ORCID: <https://orcid.org/0009-0006-9869-9455>),
  Xin Lai [aut] (ORCID: <https://orcid.org/0000-0003-4913-5822>),
  Tampere University [fnd] (PROFI6 Health Data Science program)
Maintainer: Zhesi Zhang <zhesizhang07@gmail.com>