Package: ngsReports
Version: 1.6.1
Date: 2020/11/21
Title: Load FastqQC reports and other NGS related files
Authors@R: c(
    person("Steve", "Pederson", 
        email = "stephen.pederson.au@gmail.com", role = c("aut", "cre")),
    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 
    visualising the data loaded from these files.
URL: https://github.com/steveped/ngsReports
BugReports: https://github.com/steveped/ngsReports/issues
License: file LICENSE
Encoding: UTF-8
Depends: R (>= 4.0.0), BiocGenerics, ggplot2, tibble (>= 1.3.1)
Imports: Biostrings, checkmate, dplyr (>= 1.0.0), DT, FactoMineR,
        forcats, ggdendro, grDevices, grid, lifecycle, lubridate,
        methods, pander, parallel, plotly, readr, reshape2, rmarkdown,
        Rsamtools, scales, ShortRead, stats, stringr, tidyr, tidyselect
        (>= 0.2.3), utils, viridisLite, zoo
LazyData: true
RoxygenNote: 7.1.1
Collate: 'AllGenerics.R' 'validationFunctions.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' 'plotKmers.R'
        'plotNContent.R' 'plotOverrep.R' 'plotReadTotals.R'
        'plotSeqContent.R' 'plotSeqLengthDistn.R' 'plotSeqQuals.R'
        'plotSummary.R' 'pwf.R' 'readTotals.R' 'runFastQC.R'
        'writeHtmlReport.R'
VignetteBuilder: knitr
Suggests: BiocStyle, Cairo, knitr, testthat, truncnorm
biocViews: QualityControl, ReportWriting
RdMacros: lifecycle
git_url: https://git.bioconductor.org/packages/ngsReports
git_branch: RELEASE_3_12
git_last_commit: 5f7c1da
git_last_commit_date: 2020-11-21
Date/Publication: 2020-11-21
NeedsCompilation: no
Packaged: 2020-11-22 03:18:27 UTC; biocbuild
Author: Steve Pederson [aut, cre],
  Christopher Ward [aut],
  Thu-Hien To [aut]
Maintainer: Steve Pederson <stephen.pederson.au@gmail.com>
Built: R 4.0.3; ; 2020-11-22 15:10:19 UTC; windows
