DESCRIPTION

Package: ngsReports
Version: 2.7.1
Date: 2024/07/22
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)