Package: quaqcr
Title: Quick ATAC-Seq QC
Version: 1.0.4.9000
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
Roxygen: list(markdown = TRUE, old_usage = TRUE)
RoxygenNote: 7.3.3
Suggests: testthat (>= 3.0.0)
Config/testthat/edition: 3
SystemRequirements: quaqc (https://github.com/bjmt/quaqc)
Repository: https://bjmt.r-universe.dev
Date/Publication: 2026-05-24 09:50:20 UTC
RemoteUrl: https://github.com/bjmt/quaqcr
RemoteRef: HEAD
RemoteSha: cb4a0ec40a7a378999bf97765c0358b38b65dc5c
NeedsCompilation: no
Packaged: 2026-10-06 09:00:38 UTC; root
Author: Benjamin Jean-Marie Tremblay [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-7441-2951>)
Maintainer: Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>