Package: MIRit
Title: Integrate microRNA and gene expression to decipher pathway
        complexity
Version: 1.4.0
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://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: 7.3.2
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
git_url: https://git.bioconductor.org/packages/MIRit
git_branch: RELEASE_3_21
git_last_commit: 712a0b8
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: yes
Packaged: 2025-04-16 02:02:06 UTC; biocbuild
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>
Built: R 4.5.0; x86_64-w64-mingw32; 2025-04-16 14:54:56 UTC; windows
Archs: x64
