DESCRIPTION

Package: enrichTF
Type: Package
Title: Transcription Factors Enrichment Analysis
Version: 0.99.12
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 | file LICENSE
Encoding: UTF-8
LazyData: true
Depends:
    pipeFrame
Imports:
    BSgenome,
    rtracklayer,
    motifmatchr,
    TFBSTools,
    R.utils,
    methods,
    JASPAR2018,
    GenomeInfoDb,
    GenomicRanges,
    IRanges,
    BiocGenerics,
    S4Vectors,
    utils,
    parallel,
    stats
Suggests:
    knitr,
    magrittr
Collate: 
    EnrichStep.R 
    ConnectTargetGene.R
    TFsEnrichInRegions.R
    FindMotifsInRegions.R
    GenBackground.R
    onLoad.R
    untils.R
    Method.R
RoxygenNote: 6.1.1
VignetteBuilder: knitr
biocViews: Software, GeneTarget, MotifAnnotation, GraphAndNetwork 
URL: https://github.com/wzthu/enrichTF
BugReports: https://github.com/wzthu/enrichTF/issues