Package: ATACseqTFEA
Type: Package
Title: Transcription Factor Enrichment Analysis for ATAC-seq
Version: 1.13.0
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
Config/pak/sysreqs: make libgsl0-dev libbz2-dev liblzma-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:18:13 UTC
RemoteUrl: https://github.com/bioc/ATACseqTFEA
RemoteRef: HEAD
RemoteSha: e0054eaafff91c64740e4545f22d5b29362e38a8
NeedsCompilation: no
Packaged: 2026-02-08 10:01:58 UTC; root
Author: Jianhong Ou [aut, cre] (ORCID: <https://orcid.org/0000-0002-8652-2488>)
Maintainer: Jianhong Ou <jou@morgridge.org>
Built: R 4.6.0; ; 2026-02-08 10:05:52 UTC; windows
