ATACseqTFEA
Transcription Factor Enrichment Analysis for ATAC-seq
Bioconductor version: 3.23 · Package version: 1.14.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ATACseqTFEA")Details
| Maintainer | Jianhong Ou <jou@morgridge.org> |
| Author | Jianhong Ou [aut, cre] (ORCID: <https://orcid.org/0000-0002-8652-2488>) |
| License | GPL-3 |
| URL | https://github.com/jianhong/ATACseqTFEA |
| Bug Reports | https://github.com/jianhong/ATACseqTFEA/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ATACSeq, DNASeq, GeneRegulation, MNaseSeq, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/ATACseqTFEA/ |
Citation
From within R, enter citation("ATACseqTFEA"):
Jianhong Ou. ATACseqTFEA: Transcription Factor Enrichment Analysis for ATAC-seq. doi:10.18129/B9.bioc.ATACseqTFEA, R package version 1.14.0, https://bioconductor.org/packages/ATACseqTFEA.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | ATACseqTFEA_1.14.0.tar.gz |
| Windows binary (x86_64) | ATACseqTFEA_1.14.0.zip |
| macOS binary (arm64) | ATACseqTFEA_1.14.0.tgz |
| macOS binary (x86_64) | ATACseqTFEA_1.14.0.tgz |
Dependencies
Depends: R (>= 4.2)
Imports: BiocGenerics, S4Vectors, IRanges, Matrix, GenomicRanges, GenomicAlignments, Seqinfo, SummarizedExperiment, Rsamtools, motifmatchr, TFBSTools, stats, pracma, ggplot2, ggrepel, dplyr, limma, methods, rtracklayer
Suggests: BSgenome.Drerio.UCSC.danRer10, knitr, testthat, ATACseqQC, rmarkdown, BiocStyle