ATACseqQC

DOI: 10.18129/B9.bioc.ATACseqQC  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see ATACseqQC.

ATAC-seq Quality Control

Bioconductor version: 3.17

ATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. Comparing to the other methods, ATAC-seq requires less amount of the biological samples and time to process. In the process of analyzing several ATAC-seq dataset produced in our labs, we learned some of the unique aspects of the quality assessment for ATAC-seq data.To help users to quickly assess whether their ATAC-seq experiment is successful, we developed ATACseqQC package partially following the guideline published in Nature Method 2013 (Greenleaf et al.), including diagnostic plot of fragment size distribution, proportion of mitochondria reads, nucleosome positioning pattern, and CTCF or other Transcript Factor footprints.

Author: Jianhong Ou, Haibo Liu, Feng Yan, Jun Yu, Michelle Kelliher, Lucio Castilla, Nathan Lawson, Lihua Julie Zhu

Maintainer: Jianhong Ou <jianhong.ou at duke.edu>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("ATACseqQC")

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("ATACseqQC")

 

HTML	R Script	ATACseqQC Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	ATACSeq, Coverage, DNASeq, GeneRegulation, ImmunoOncology, NucleosomePositioning, QualityControl, Sequencing, Software
Version	1.24.0
In Bioconductor since	BioC 3.5 (R-3.4) (6.5 years)
License	GPL (>= 2)
Depends	R (>= 3.5.0), BiocGenerics, S4Vectors
Imports	BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges, GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid, limma, Rsamtools(>= 1.31.2), randomForest, rtracklayer, stats, motifStack, preseqR, utils, KernSmooth, edgeR
LinkingTo
Suggests	BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	NADfinder
Suggests Me	ATACseqTFEA
Links To Me
Build Report

Package Archives

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

Source Package	ATACseqQC_1.24.0.tar.gz
Windows Binary	ATACseqQC_1.24.0.zip
macOS Binary (x86_64)	ATACseqQC_1.24.0.tgz
macOS Binary (arm64)	ATACseqQC_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ATACseqQC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ATACseqQC
Bioc Package Browser	https://code.bioconductor.org/browse/ATACseqQC/
Package Short Url	https://bioconductor.org/packages/ATACseqQC/
Package Downloads Report	Download Stats