Please cite the paper below for the ATACseqQC package.

Ou J, Liu H, Yu J, Kelliher MA, Castilla LH, Lawson ND, Zhu LJ. ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data. BMC Genomics. 2018 Mar 1;19(1):169.<doi:10.1186/s12864-018-4559-3>. PubMed PMID:29490630.

Corresponding BibTeX entry:

  @Article{,
    title = {ATACseqQC: a Bioconductor package for post-alignment
      quality assessment of ATAC-seq data},
    author = {Jianhong Ou and Haibo Liu and Jun Yu and Michelle A.
      Kelliher and Lucio H. Castilla and Nathan D. Lawson and Lihua
      Julie Zhu},
    journal = {BMC Genomics},
    year = {2018},
    month = {Mar},
    day = {01},
    volume = {19},
    number = {1},
    pages = {169},
    url = {https://doi.org/10.1186/s12864-018-4559-3},
    doi = {10.1186/s12864-018-4559-3},
    pubmedid = {29490630},
    issn = {1471-2164},
    abstract = {ATAC-seq (Assays for Transposase-Accessible Chromatin
      using sequencing) is a recently developed technique for
      genome-wide analysis of chromatin accessibility. Compared to
      earlier methods for assaying chromatin accessibility, ATAC-seq is
      faster and easier to perform, does not require cross-linking, has
      higher signal to noise ratio, and can be performed on small cell
      numbers. However, to ensure a successful ATAC-seq experiment,
      step-by-step quality assurance processes, including both wet lab
      quality control and in silico quality assessment, are essential.
      While several tools have been developed or adopted for assessing
      read quality, identifying nucleosome occupancy and accessible
      regions from ATAC-seq data, none of the tools provide a
      comprehensive set of functionalities for preprocessing and
      quality assessment of aligned ATAC-seq datasets.},
  }