ATACseqTFEA

DOI: 10.18129/B9.bioc.ATACseqTFEA  

Transcription Factor Enrichment Analysis for ATAC-seq

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

HTML	R Script	ATACseqTFEA Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	ATACSeq, DNASeq, GeneRegulation, MNaseSeq, Sequencing, Software
Version	1.0.1
In Bioconductor since	BioC 3.16 (R-4.2) (< 6 months)
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
LinkingTo
Suggests	BSgenome.Drerio.UCSC.danRer10, knitr, testthat, ATACseqQC, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/jianhong/ATACseqTFEA
BugReports	https://github.com/jianhong/ATACseqTFEA/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	ATACseqTFEA_1.0.1.tar.gz
Windows Binary	ATACseqTFEA_1.0.1.zip
macOS Binary (x86_64)	ATACseqTFEA_1.0.1.tgz
macOS Binary (arm64)	ATACseqTFEA_1.0.1.tgz
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
Old Source Packages for BioC 3.16	Source Archive