Package: quaqcr
Title: Quick ATAC-Seq QC
Version: 1.0.4
Authors@R: 
    person(c("Benjamin", "Jean-Marie"), "Tremblay", role = c("aut", "cre"),
      email = "benjmtremblay@gmail.com",
      comment = c(ORCID = "0000-0002-7441-2951"))
Description: A wrapper around the 'quaqc' program described in Tremblay and
    Questa (2024) <doi:10.1093/bioinformatics/btae649>. 'quaqc' allows for
    assay for transposase-accessible chromatin using sequencing (ATAC-seq)
    specific quality control and read filtering of next-generation sequencing
    (NGS) data with minimal processing time and extremely low memory overhead.
    Any number of samples can be processed, using multiple threads if desired.
    'quaqc' outputs a comprehensive set of aligned read metrics, including
    alignment size, fragment size, percent duplicates, mapq scores, read depth,
    GC content, and others. Although designed for ATAC-seq data, 'quaqc' can
    also be used for other unspliced DNA sequencing experiments (such as
    chromatin immunoprecipitation sequencing, or ChIP-seq) as many of the
    metrics are related to general sequencing quality. This R package also
    provides additional utilities for custom analyses and plotting of 'quaqc'
    results.
URL: https://github.com/bjmt/quaqcr
BugReports: https://github.com/bjmt/quaqcr/issues
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 3.6.0)
Imports: methods, utils, jsonlite
RoxygenNote: 7.3.3
Suggests: testthat (>= 3.0.0)
Config/testthat/edition: 3
SystemRequirements: quaqc (https://github.com/bjmt/quaqc)
NeedsCompilation: no
Packaged: 2026-05-15 10:04:43 UTC; gok24jef
Author: Benjamin Jean-Marie Tremblay [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-7441-2951>)
Maintainer: Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
Repository: CRAN
Date/Publication: 2026-05-19 09:30:02 UTC
Built: R 4.4.3; ; 2026-05-19 12:05:58 UTC; unix
