DOI: 10.18129/B9.bioc.ATACseqQC    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see ATACseqQC.

ATAC-seq Quality Control

Bioconductor version: 3.10

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>

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biocViews ATACSeq, Coverage, DNASeq, GeneRegulation, ImmunoOncology, NucleosomePositioning, QualityControl, Sequencing, Software
Version 1.10.4
In Bioconductor since BioC 3.5 (R-3.4) (3 years)
License GPL (>= 2)
Depends R (>= 3.4), 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
Suggests BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat
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