Package: RegEnrich
Type: Package
Title: Gene regulator enrichment analysis
Version: 1.21.0
Authors@R: c(
    person("Weiyang", "Tao", email = "weiyangtao1513@gmail.com", 
        role = c("cre", "aut")),
    person("Aridaman", "Pandit", email = "A.Pandit@umcutrecht.nl", 
        role = "aut"))
Description: This package is a pipeline to identify the key gene regulators in a biological 
    process, for example in cell differentiation and in cell development after stimulation. 
    There are four major steps in this pipeline: (1) differential expression analysis; (2) 
    regulator-target network inference; (3) enrichment analysis; and (4) regulators scoring 
    and ranking.
Depends: 
    R (>= 4.0.0),
    S4Vectors,
    dplyr,
    tibble,
    BiocSet,
    SummarizedExperiment
License: GPL (>= 2)
Encoding: UTF-8
VignetteBuilder: knitr
RoxygenNote: 7.3.1
Collate: 
    'COEN.R'
    'globals.R'
    'DEA.R'
    'GRN.R'
    'data.R'
    'regenrichClasses.R'
    'genericMethods.R'
    'localUtils.R'
    'plots.R'
    'regFET.R'
    'regSEA.R'
    'regenrich_diffExpr.R'
    'regenrich_enrich.R'
    'regenrich_network.R'
    'regenrich_rankScore.R'
    'results.R'
    'show.R'
    'topNet.R'
Imports: 
    randomForest,
    fgsea,
    DOSE,
    BiocParallel,
    DESeq2,
    limma,
    WGCNA,
    ggplot2 (>= 2.2.0),
    methods,
    reshape2,
    magrittr,
    BiocStyle
Suggests: 
    GEOquery,
    rmarkdown,
    knitr,
    BiocManager,
    testthat
biocViews:
    GeneExpression, Transcriptomics, RNASeq, TwoChannel, 
    Transcription, GeneTarget, NetworkEnrichment,
    DifferentialExpression, Network, NetworkInference,
    GeneSetEnrichment, FunctionalPrediction
git_url: https://git.bioconductor.org/packages/RegEnrich
git_branch: devel
git_last_commit: 73e2009
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
