ATACseqQC

DOI: 10.18129/B9.bioc.ATACseqQC    

ATAC-seq Quality Control

Bioconductor version: Release (3.6)

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, Jun Yu, Haibo Liu, Michelle Kelliher, Lucio Castilla, Nathan Lawson, Lihua Julie Zhu

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ATACseqQC")

Documentation

HTML	R Script	ATACseqQC Vignette
PDF		Reference Manual

Details

biocViews	ATACSeq, Coverage, DNASeq, GeneRegulation, NucleosomePositioning, QualityControl, Sequencing, Software
Version	1.2.10
In Bioconductor since	BioC 3.5 (R-3.4) (1 year)
License	GPL (>= 2)
Depends	R (>= 3.4), BiocGenerics, S4Vectors
Imports	BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges, GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid, limma, Rsamtools, randomForest, rtracklayer, stats, motifStack
LinkingTo
Suggests	utils, BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	ATACseqQC_1.2.10.tar.gz
Windows Binary	ATACseqQC_1.2.10.zip
Mac OS X 10.11 (El Capitan)	ATACseqQC_1.2.10.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ATACseqQC
Package Short Url	http://bioconductor.org/packages/ATACseqQC/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive