Package: ATACseqTFEA Type: Package Title: Transcription Factor Enrichment Analysis for ATAC-seq Version: 1.15.0 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: 2026-04-28 12:58:51 UTC RemoteUrl: https://github.com/bioc/ATACseqTFEA RemoteRef: HEAD RemoteSha: 4089814b290298b12014bc38f266c2f8dc338472 NeedsCompilation: no Packaged: 2026-05-28 14:43:18 UTC; root Author: Jianhong Ou [aut, cre] (ORCID: ) Maintainer: Jianhong Ou