RegEnrich

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• Repository: https://github.com/WeiyangTao/RegEnrich

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[bioc-issue-bot]

Hi @WeiyangTao

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: RegEnrich
Type: Package
Title: Gene regulator enrichment analysis
Version: 0.99.1
Author: Weiyang Tao<w.tao-2@umcutrecht.nl>, 
        Timothy R.D.J. Radstakec, 
        Aridaman Pandit<A.Pandit@umcutrecht.nl>
Maintainer: Weiyang Tao <w.tao-2@umcutrecht.nl>
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)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 7.0.2
Collate: 
    'globals.R'
    'COEN.R'
    'DEA.R'
    'GRN.R'
    'data.R'
    'localUtils.R'
    'regenrichClasses.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,
    ggplot2 (>= 2.2.0),
    fgsea,
    DOSE,
    BiocParallel,
    DESeq2,
    limma,
    WGCNA,
    S4Vectors,
    SummarizedExperiment,
    data.table,
    reshape2,
    methods
Suggests: 
    GEOquery,
    dplyr,
    rmarkdown,
    knitr,
    BiocManager,
    testthat
biocViews:
    GeneExpression, Transcriptomics, RNASeq, TwoChannel, 
    Transcription, GeneTarget, NetworkEnrichment,
    DifferentialExpression, Network,
    GeneSetEnrichment, FunctionalPrediction,