Package: ATACseqQC Type: Package Title: ATAC-seq Quality Control Version: 1.37.1 Author: Jianhong Ou, Haibo Liu, Feng Yan, Jun Yu, Michelle Kelliher, Lucio Castilla, Chao Deng, Nathan Lawson, Lihua Julie Zhu Maintainer: Jianhong Ou Description: 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. Depends: R (>= 3.5.0), BiocGenerics, S4Vectors Imports: BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges, GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid, limma, polynom, Rsamtools (>= 1.31.2), randomForest, rtracklayer, stats, motifStack, utils, KernSmooth, edgeR, BiocParallel Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat, rmarkdown License: GPL (>= 2) VignetteBuilder: knitr RoxygenNote: 8.0.0 biocViews: Sequencing, DNASeq, ATACSeq, GeneRegulation, QualityControl, Coverage, NucleosomePositioning, ImmunoOncology Encoding: UTF-8 Config/pak/sysreqs: cmake make libgsl0-dev libbz2-dev libicu-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev xz-utils zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-06-24 20:25:34 UTC RemoteUrl: https://github.com/bioc/ATACseqQC RemoteRef: HEAD RemoteSha: 43c8082cb96936f74b5553fd264d8a4e90a46904 NeedsCompilation: no Packaged: 2026-06-25 11:49:19 UTC; root