ATACseqTFEA

DOI: 10.18129/B9.bioc.ATACseqTFEA    

This is the development version of ATACseqTFEA; to use it, please install the devel version of Bioconductor.

Transcription Factor Enrichment Analysis for ATAC-seq

Bioconductor version: Development (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>

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

Installation

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

 

HTML R Script ATACseqTFEA Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews ATACSeq, DNASeq, GeneRegulation, MNaseSeq, Sequencing, Software
Version 0.99.11
In Bioconductor since BioC 3.16 (R-4.2)
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_0.99.11.tar.gz
Windows Binary ATACseqTFEA_0.99.11.zip
macOS Binary (x86_64) ATACseqTFEA_0.99.11.tgz
macOS Binary (arm64) ATACseqTFEA_0.99.11.tgz
Source Repository git clone https://git.bioconductor.org/packages/ATACseqTFEA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ATACseqTFEA
Package Short Url https://bioconductor.org/packages/ATACseqTFEA/
Package Downloads Report Download Stats

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