ATACseqTFEA

This is the development version of ATACseqTFEA; for the stable release version, see ATACseqTFEA.

Transcription Factor Enrichment Analysis for ATAC-seq

Bioconductor version: Development (3.21)

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] (ORCID: )

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

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ATACseqTFEA")

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

Documentation

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

browseVignettes("ATACseqTFEA")

ATACseqTFEA Vignette	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ATACSeq, DNASeq, GeneRegulation, MNaseSeq, Sequencing, Software
Version	1.9.0
In Bioconductor since	BioC 3.16 (R-4.2) (2 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, rtracklayer
System Requirements
URL	https://github.com/jianhong/ATACseqTFEA
Bug Reports	https://github.com/jianhong/ATACseqTFEA/issues

Suggests	BSgenome.Drerio.UCSC.danRer10, knitr, testthat, ATACseqQC, rmarkdown, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ATACseqTFEA_1.9.0.tar.gz
Windows Binary (x86_64)	ATACseqTFEA_1.9.0.zip
macOS Binary (x86_64)
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/
Package Downloads Report	Download Stats