This is the development version of ATACseqTFEA; for the stable release version, see ATACseqTFEA.
Transcription Factor Enrichment Analysis for ATAC-seqBioconductor version: Development (3.22)
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: 0000-0002-8652-2488
Maintainer: Jianhong Ou <jou at morgridge.org>
Citation (from within R, entercitation("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.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ATACseqTFEA")Follow Installation instructions to use this package in your R session.
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