Package: PanomiR
Title: Detection of miRNAs that regulate interacting groups of pathways
Version: 1.0.2
Authors@R: c(
    person("Pourya", "Naderi", email = "pouryany@gmail.com",
           role = c("aut", "cre")),
    person("Yue Yang (Alan)", "Teo", email = "yueyang.teo@epfl.ch",
           role = c("aut")),
    person("Ilya", "Sytchev", email = "isytchev@hsph.harvard.edu",
           role = c("aut")),
    person("Winston", "Hide", email = "whide@bidmc.harvard.edu",
           role = c("aut")))
Description: PanomiR is a package to detect miRNAs that target groups of
    pathways from gene expression data. This package provides functionality 
    for generating pathway activity profiles, determining differentially
    activated pathways between user-specified conditions, determining 
    clusters of pathways via the PCxN package, and generating miRNAs targeting
    clusters of pathways. These function can be used separately or sequentially
    to analyze RNA-Seq data.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.1.2
Suggests:
    testthat (>= 3.0.0),
    BiocStyle,
    knitr,
    rmarkdown
Config/testthat/edition: 3
biocViews: GeneExpression, GeneSetEnrichment, GeneTarget, miRNA, Pathways
Imports:
    clusterProfiler,
    dplyr,
    forcats,
    GSEABase,
    igraph,
    limma,
    metap,
    org.Hs.eg.db,
    parallel,
    preprocessCore,
    RColorBrewer,
    rlang,
    tibble,
    withr,
    utils
Depends:
    R (>= 4.2.0)
URL: https://github.com/pouryany/PanomiR
BugReports: https://github.com/pouryany/PanomiR/issues
VignetteBuilder: knitr