Package: ngsReports
Version: 2.12.1
Date: 2025/11/09
Title: Load FastqQC reports and other NGS related files
Authors@R: c(
    person("Stevie", "Pederson", 
        email = "stephen.pederson.au@gmail.com", role = c("aut", "cre"),
        comment = c(ORCID = "0000-0001-8197-3303")
        ),
    person("Christopher", "Ward", 
        email = "christopher.ward@adelaide.edu.au", role = c("aut")),
    person("Thu-Hien", "To", email = "tothuhien@gmail.com", role = c("aut"))
    )
Description: This package provides methods and object classes for
        parsing FastQC reports and output summaries from other NGS
        tools into R. As well as parsing files, multiple plotting
        methods have been implemented for visualising the parsed data.
        Plots can be generated as static ggplot objects or interactive
        plotly objects.
URL: https://github.com/smped/ngsReports
BugReports: https://github.com/smped/ngsReports/issues
License: LGPL-3
Encoding: UTF-8
Depends: R (>= 4.2.0), BiocGenerics, ggplot2 (>= 4.0.0), patchwork (>=
        1.1.1), tibble (>= 1.3.1)
Imports: Biostrings, checkmate, dplyr (>= 1.1.0), forcats, ggdendro,
        grDevices (>= 3.6.0), grid, jsonlite, lifecycle, lubridate,
        methods, plotly (>= 4.9.4), rlang, rmarkdown, scales, stats,
        stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo
LazyData: true
RoxygenNote: 7.3.3
Collate: 'AllGenerics.R' 'validationFunctions.R' 'FastpData.R'
        'FastpDataList.R' 'FastpFile.R' 'FastqcData.R'
        'FastqcDataList.R' 'FastqcFile.R' 'PwfCols.R' 'S4coercion.R'
        'TheoreticalGC.R' 'aaa.R' 'data.R' 'errMsg.R' 'estGcDistn.R'
        'extract.R' 'fqName.R' 'fqcVersion.R' 'getColours.R' 'getGC.R'
        'getModule.R' 'getSummary.R' 'helpers.R' 'importNgsLogs.R'
        'importSJ.R' 'isCompressed.R' 'maxAdapterContent.R'
        'ngsReports-package.R' 'overRep2Fasta.R' 'path.R'
        'plotAdapterContent.R' 'plotAlignmentSummary.R'
        'plotAssemblyStats.R' 'plotBaseQuals.R' 'plotDupLevels.R'
        'plotFastqcPCA.R' 'plotGcContent.R' 'plotInsertSize.R'
        'plotKmers.R' 'plotNContent.R' 'plotOverrep.R'
        'plotReadTotals.R' 'plotSeqContent.R' 'plotSeqLengthDistn.R'
        'plotSeqQuals.R' 'plotSummary.R' 'pwf.R' 'readTotals.R'
        'summariseOverrep.R' 'writeHtmlReport.R'
VignetteBuilder: knitr
Suggests: BiocStyle, Cairo, DT, knitr, pander, readr, testthat,
        truncnorm
biocViews: QualityControl, ReportWriting
RdMacros: lifecycle
Roxygen: list(markdown = TRUE)
Config/pak/sysreqs: make libicu-dev libssl-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-11-09 08:26:06 UTC
RemoteUrl: https://github.com/bioc/ngsReports
RemoteRef: RELEASE_3_22
RemoteSha: 61929781284d956c973600f80b1c82bf05b10cdf
NeedsCompilation: no
Packaged: 2025-11-11 16:10:28 UTC; root
Author: Stevie Pederson [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8197-3303>),
  Christopher Ward [aut],
  Thu-Hien To [aut]
Maintainer: Stevie Pederson <stephen.pederson.au@gmail.com>
Built: R 4.5.2; ; 2025-11-11 16:14:54 UTC; windows
