Package: ngsReports
Version: 2.10.0
Date: 2025/03/01
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 (>= 3.5.0), 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), reshape2, rlang, rmarkdown, scales,
        stats, stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo
LazyData: true
RoxygenNote: 7.3.2
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)
git_url: https://git.bioconductor.org/packages/ngsReports
git_branch: RELEASE_3_21
git_last_commit: 33b9e03
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-16 02:26:03 UTC; biocbuild
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 4.5.0; ; 2025-04-16 15:02:47 UTC; windows
