Package: RegEnrich
Type: Package
Title: Gene regulator enrichment analysis
Version: 1.20.0
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
Config/pak/sysreqs: make libicu-dev libpng-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:00:04 UTC
RemoteUrl: https://github.com/bioc/RegEnrich
RemoteRef: RELEASE_3_22
RemoteSha: 48330322fc3ef0eb0531c88e12e9a76d36524c17
NeedsCompilation: no
Packaged: 2026-02-23 10:04:27 UTC; root
Author: Weiyang Tao [cre, aut],
  Aridaman Pandit [aut]
Maintainer: Weiyang Tao <weiyangtao1513@gmail.com>
Built: R 4.5.2; ; 2026-02-23 10:06:58 UTC; windows
