DESCRIPTION

Package: enrichTF
Type: Package
Title: Transcription Factors Enrichment Analysis
Version: 1.3.5
Author: Zheng Wei, Zhana Duren, Shining Ma
Maintainer: Zheng Wei <wzwz@stanford.edu>
Description: As transcription factors (TFs) 
    play a crucial role in regulating the 
    transcription process through binding on the 
    genome alone or in a combinatorial manner, 
    TF enrichment analysis is an efficient and important procedure to
    locate the candidate functional TFs from a set of experimentally 
    defined regulatory regions. 
    While it is commonly accepted that structurally 
    related TFs may have similar binding preference to sequences (i.e. motifs) 
    and one TF may have multiple motifs, TF enrichment analysis is much more 
    challenging than motif enrichment analysis. Here we present a R package 
    for TF enrichment analysis 
    which combine motif enrichment with the PECA model.
License: GPL-3 
Encoding: UTF-8
LazyData: FALSE
Depends:
    pipeFrame
Imports:
    BSgenome,
    rtracklayer,
    motifmatchr,
    TFBSTools,
    R.utils,
    methods,
    JASPAR2018,
    GenomeInfoDb,
    GenomicRanges,
    IRanges,
    BiocGenerics,
    S4Vectors,
    utils,
    parallel,
    stats,
    ggpubr,
    heatmap3,
    ggplot2,
    clusterProfiler,
    rmarkdown,
    grDevices,
    magrittr
Suggests:
    knitr,
    testthat,
    webshot
Collate: 
    EnrichStep.R 
    ConnectTargetGene.R
    TFsEnrichInRegions.R
    FindMotifsInRegions.R
    UnzipAndMergeBed.R
    TissueOpennessSpecificity.R
    TissueOpennessConserve.R
    SingleSampleReport.R
    GenBackground.R
    onLoad.R
    untils.R
    Method.R
    GeneOntology.R
RoxygenNote: 7.0.2
VignetteBuilder: knitr
biocViews: Software, GeneTarget, MotifAnnotation, GraphAndNetwork, Transcription  
URL: https://github.com/wzthu/enrichTF
BugReports: https://github.com/wzthu/enrichTF/issues