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Transcription Factor Enrichment Analysis for ATAC-seq

Bioconductor version: Release (3.18)

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.

Author: Jianhong Ou [aut, cre]

Maintainer: Jianhong Ou <jianhong.ou at duke.edu>

Citation (from within R, enter citation("ATACseqTFEA")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

ATACseqTFEA Vignette HTML R Script
Reference Manual PDF


biocViews ATACSeq, DNASeq, GeneRegulation, MNaseSeq, Sequencing, Software
Version 1.4.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License GPL-3
Depends R (>= 4.2)
Imports BiocGenerics, S4Vectors, IRanges, Matrix, GenomicRanges, GenomicAlignments, GenomeInfoDb, SummarizedExperiment, Rsamtools, motifmatchr, TFBSTools, stats, pracma, ggplot2, ggrepel, dplyr, limma, methods
System Requirements
URL https://github.com/jianhong/ATACseqTFEA
Bug Reports https://github.com/jianhong/ATACseqTFEA/issues
See More
Suggests BSgenome.Drerio.UCSC.danRer10, knitr, testthat, ATACseqQC, rmarkdown, BiocStyle
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Follow Installation instructions to use this package in your R session.

Source Package ATACseqTFEA_1.4.0.tar.gz
Windows Binary ATACseqTFEA_1.4.0.zip
macOS Binary (x86_64) ATACseqTFEA_1.4.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/ATACseqTFEA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ATACseqTFEA
Bioc Package Browser https://code.bioconductor.org/browse/ATACseqTFEA/
Package Short Url https://bioconductor.org/packages/ATACseqTFEA/
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