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ATACseqTFEA
This is thereleased version of ATACseqTFEA; for the devel version, seeATACseqTFEA.
Transcription Factor Enrichment Analysis for ATAC-seq
Bioconductor version: Release (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("ATACseqTFEA")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("ATACseqTFEA")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text |
Details
| biocViews | ATACSeq,DNASeq,GeneRegulation,MNaseSeq,Sequencing,Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (3 years) |
| License | GPL-3 |
| Depends | R (>= 4.2) |
| Imports | BiocGenerics,S4Vectors,IRanges,Matrix,GenomicRanges,GenomicAlignments,Seqinfo,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 |
See More
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | ATACseqTFEA_1.12.0.tar.gz |
| Windows Binary (x86_64) | ATACseqTFEA_1.12.0.zip (64-bit only) |
| macOS Binary (x86_64) | ATACseqTFEA_1.12.0.tgz |
| macOS Binary (arm64) | ATACseqTFEA_1.12.0.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 |