Package: RegEnrich
Type: Package
Title: Gene regulator enrichment analysis
Version: 1.0.0
Authors@R: c(
    person("Weiyang", "Tao", email = "w.tao-2@umcutrecht.nl", 
        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: 7.1.1
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
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: RELEASE_3_12
git_last_commit: 4a03b2e
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-27
NeedsCompilation: no
Packaged: 2020-10-28 02:52:19 UTC; biocbuild
Author: Weiyang Tao [cre, aut],
  Aridaman Pandit [aut]
Maintainer: Weiyang Tao <w.tao-2@umcutrecht.nl>
Built: R 4.0.3; ; 2020-11-02 08:25:33 UTC; unix
