Package: ATACseqTFEA
Type: Package
Title: Transcription Factor Enrichment Analysis for ATAC-seq
Version: 1.11.1
Authors@R: person(given="Jianhong", family="Ou", email="jou@morgridge.org", 
    role=c("aut", "cre"), comment=c(ORCID="0000-0002-8652-2488"))
Description: Assay for Transpose-Accessible Chromatin using sequencing
    (ATAC-seq) is a technique to assess genome-wide chromatin accessibility
    by probing open chromatin with hyperactive mutant Tn5 Transposase that
    inserts sequencing adapters into open regions of the genome.
    ATACseqTFEA is an improvement of the current computational method that
    detects differential activity of transcription factors (TFs).
    ATACseqTFEA not only uses the difference of open region information,
    but also (or emphasizes) the difference of TFs
    footprints (cutting sites or insertion sites).
    ATACseqTFEA provides an easy, rigorous way to broadly assess TF
    activity changes between two conditions.
BugReports: https://github.com/jianhong/ATACseqTFEA/issues
URL: https://github.com/jianhong/ATACseqTFEA
Depends: R (>= 4.2)
Imports: BiocGenerics, S4Vectors, IRanges, Matrix, GenomicRanges,
        GenomicAlignments, Seqinfo, SummarizedExperiment, Rsamtools,
        motifmatchr, TFBSTools, stats, pracma, ggplot2, ggrepel, dplyr,
        limma, methods, rtracklayer
Suggests: BSgenome.Drerio.UCSC.danRer10, knitr, testthat, ATACseqQC,
        rmarkdown, BiocStyle
biocViews: Sequencing, DNASeq, ATACSeq, MNaseSeq, GeneRegulation
License: GPL-3
Encoding: UTF-8
VignetteBuilder: knitr
RoxygenNote: 7.2.3
git_url: https://git.bioconductor.org/packages/ATACseqTFEA
git_branch: devel
git_last_commit: fc5eeae
git_last_commit_date: 2025-07-22
Repository: Bioconductor 3.22
Date/Publication: 2025-07-23
NeedsCompilation: no
Packaged: 2025-07-23 21:29:29 UTC; biocbuild
Author: Jianhong Ou [aut, cre] (ORCID: <https://orcid.org/0000-0002-8652-2488>)
Maintainer: Jianhong Ou <jou@morgridge.org>
Built: R 4.5.1; ; 2025-07-24 12:36:38 UTC; windows
