Package: MIRit
Title: Integrate microRNA and gene expression to decipher pathway
        complexity
Version: 1.9.0
Date: 2023-11-23
Authors@R: c(
    person("Jacopo", "Ronchi", email = "jacopo.ronchi@unimib.it",
           role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5520-4631")),
    person("Maria", "Foti", email = "maria.foti@unimib.it",
           role = c("fnd"), comment = c(ORCID = "0000-0002-4481-1900")))
Description: 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.
License: GPL (>= 3)
URL: https://jacopo-ronchi.github.io/MIRit/,
        https://github.com/jacopo-ronchi/MIRit
BugReports: https://github.com/jacopo-ronchi/MIRit/issues
biocViews: Software, GeneRegulation, NetworkEnrichment,
        NetworkInference, Epigenetics, FunctionalGenomics,
        SystemsBiology, Network, Pathways, GeneExpression,
        DifferentialExpression
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Imports: AnnotationDbi, BiocFileCache, BiocParallel, DESeq2, edgeR,
        fgsea, genekitr, geneset, ggplot2, ggpubr, graph, graphics,
        graphite, grDevices, httr, limma, methods, Rcpp, Rgraphviz (>=
        2.44.0), rlang, stats, utils
Collate: 'AllGenerics.R' 'AllClasses.R' 'MIRit-package.R'
        'RcppExports.R' 'association.R' 'batch-correction.R' 'data.R'
        'differential-expression.R' 'enrichment.R' 'integration.R'
        'show-methods.R' 'targets.R' 'topological-integration.R'
        'utils.R' 'visualization.R'
Suggests: BiocStyle, biomaRt, BSgenome.Hsapiens.UCSC.hg38,
        GenomicRanges, ggrepel, ggridges, Gviz, gwasrapidd, knitr,
        MonoPoly, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0)
Depends: MultiAssayExperiment, R (>= 4.4.0)
LazyData: false
VignetteBuilder: knitr
Config/testthat/edition: 3
LinkingTo: Rcpp
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:02:17 UTC
RemoteUrl: https://github.com/bioc/MIRit
RemoteRef: HEAD
RemoteSha: 116078895be27e9504c3381bb5705bbe1e52b580
NeedsCompilation: yes
Packaged: 2026-07-04 00:54:34 UTC; root
Author: Jacopo Ronchi [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-5520-4631>),
  Maria Foti [fnd] (ORCID: <https://orcid.org/0000-0002-4481-1900>)
Maintainer: Jacopo Ronchi <jacopo.ronchi@unimib.it>