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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "ATACseqQC" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'ATACseqQC: ATAC-seq Quality Control'
version: 1.29.0
doi: 10.1186/s12864-018-4559-3
abstract: 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.
authors:
- family-names: Ou
  given-names: Jianhong
  email: jianhong.ou@duke.edu
- family-names: Liu
  given-names: Haibo
- family-names: Yan
  given-names: Feng
- family-names: Yu
  given-names: Jun
- family-names: Kelliher
  given-names: Michelle
- family-names: Castilla
  given-names: Lucio
- family-names: Lawson
  given-names: Nathan
- family-names: Zhu
  given-names: Lihua Julie
preferred-citation:
  type: article
  title: 'ATACseqQC: a Bioconductor package for post-alignment quality assessment
    of ATAC-seq data'
  authors:
  - family-names: Ou
    given-names: Jianhong
    email: jianhong.ou@duke.edu
  - family-names: Liu
    given-names: Haibo
  - family-names: Yu
    given-names: Jun
  - family-names: Kelliher
    given-names: Michelle A.
  - family-names: Castilla
    given-names: Lucio H.
  - family-names: Lawson
    given-names: Nathan D.
  - family-names: Zhu
    given-names: Lihua Julie
  journal: BMC Genomics
  year: '2018'
  month: '3'
  volume: '19'
  issue: '1'
  url: https://doi.org/10.1186/s12864-018-4559-3
  doi: 10.1186/s12864-018-4559-3
  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.
  start: '169'
repository: https://bioc.r-universe.dev
contact:
- family-names: Ou
  given-names: Jianhong
  email: jianhong.ou@duke.edu