{
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  "Package": "ngsReports",
  "Version": "2.15.0",
  "Date": "2025/11/9",
  "Title": "Load FastqQC reports and other NGS related files",
  "Authors@R": "c(\nperson(\"Stevie\", \"Pederson\",\nemail = \"stephen.pederson.au@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-8197-3303\")\n),\nperson(\"Christopher\", \"Ward\",\nemail = \"christopher.ward@adelaide.edu.au\", role = c(\"aut\")),\nperson(\"Thu-Hien\", \"To\", email = \"tothuhien@gmail.com\", role = c(\"aut\"))\n)",
  "Description": "This package provides methods and object classes for\nparsing FastQC reports and output summaries from other NGS\ntools into R. As well as parsing files, multiple plotting\nmethods have been implemented for visualising the parsed data.\nPlots can be generated as static ggplot objects or interactive\nplotly objects.",
  "URL": "https://github.com/smped/ngsReports",
  "BugReports": "https://github.com/smped/ngsReports/issues",
  "License": "LGPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.3",
  "Collate": "'AllGenerics.R' 'validationFunctions.R' 'FastpData.R'\n'FastpDataList.R' 'FastpFile.R' 'FastqcData.R'\n'FastqcDataList.R' 'FastqcFile.R' 'PwfCols.R' 'S4coercion.R'\n'TheoreticalGC.R' 'aaa.R' 'data.R' 'errMsg.R' 'estGcDistn.R'\n'extract.R' 'fqName.R' 'fqcVersion.R' 'getColours.R' 'getGC.R'\n'getModule.R' 'getSummary.R' 'helpers.R' 'importNgsLogs.R'\n'importSJ.R' 'isCompressed.R' 'maxAdapterContent.R'\n'ngsReports-package.R' 'overRep2Fasta.R' 'path.R'\n'plotAdapterContent.R' 'plotAlignmentSummary.R'\n'plotAssemblyStats.R' 'plotBaseQuals.R' 'plotDupLevels.R'\n'plotFastqcPCA.R' 'plotGcContent.R' 'plotInsertSize.R'\n'plotKmers.R' 'plotNContent.R' 'plotOverrep.R'\n'plotReadTotals.R' 'plotSeqContent.R' 'plotSeqLengthDistn.R'\n'plotSeqQuals.R' 'plotSummary.R' 'pwf.R' 'readTotals.R'\n'summariseOverrep.R' 'writeHtmlReport.R'",
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  "Roxygen": "list(markdown = TRUE)",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:49:57 UTC",
  "RemoteUrl": "https://github.com/bioc/ngsReports",
  "RemoteRef": "HEAD",
  "RemoteSha": "fce6c797b0af0e0afbe5c54d3ba0f88fe1d24f80",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:36:30 UTC",
    "User": "root"
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  "Author": "Stevie Pederson [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-8197-3303>),\nChristopher Ward [aut],\nThu-Hien To [aut]",
  "Maintainer": "Stevie Pederson <stephen.pederson.au@gmail.com>",
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  "_published": "2026-05-30T13:31:40.603Z",
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
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  "_homeurl": "https://github.com/smped/ngsreports",
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  "_exports": [
    "estGcDistn",
    "FastpData",
    "FastpDataList",
    "FastqcData",
    "FastqcDataList",
    "fqcVersion",
    "fqName",
    "fqName<-",
    "gcAvail",
    "getColours",
    "getGC",
    "getModule",
    "getSummary",
    "importNgsLogs",
    "importSJ",
    "isCompressed",
    "maxAdapterContent",
    "mData",
    "overRep2Fasta",
    "path",
    "plotAdapterContent",
    "plotAlignmentSummary",
    "plotAssemblyStats",
    "plotBaseQuals",
    "plotDupLevels",
    "plotFastqcPCA",
    "plotGcContent",
    "plotInsertSize",
    "plotKmers",
    "plotNContent",
    "plotOverrep",
    "plotReadTotals",
    "plotSeqContent",
    "plotSeqLengthDistn",
    "plotSeqQuals",
    "plotSummary",
    "pwf",
    "readTotals",
    "setAlpha",
    "setColours",
    "summariseOverrep",
    "writeHtmlReport"
  ],
  "_datasets": [
    {
      "name": "gcTheoretical",
      "title": "Theoretical GC content",
      "object": "gcTheoretical",
      "class": [
        "TheoreticalGC"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "extract-methods",
      "title": "Extract Elements",
      "topics": [
        "[,FastpDataList,ANY,missing-method",
        "[,FastpDataList,character,missing-method",
        "[,FastpDataList,logical,missing-method",
        "[,FastpDataList,numeric,missing-method",
        "[,FastqcDataList,ANY,missing-method",
        "[,FastqcDataList,character,missing-method",
        "[,FastqcDataList,logical,missing-method",
        "[,FastqcDataList,numeric,missing-method"
      ]
    },
    {
      "page": "estGcDistn",
      "title": "Estimate a GC Content Distribution From Sequences",
      "topics": [
        "estGcDistn",
        "estGcDistn,ANY-method",
        "estGcDistn,character-method",
        "estGcDistn,DNAStringSet-method"
      ]
    },
    {
      "page": "FastpData",
      "title": "The FastpData Object Class",
      "topics": [
        "FastpData",
        "FastpData-class"
      ]
    },
    {
      "page": "FastpDataList",
      "title": "The FastpDataList Object Class",
      "topics": [
        "FastpDataList",
        "FastpDataList-class"
      ]
    },
    {
      "page": "FastqcData",
      "title": "The FastqcData Object Class",
      "topics": [
        "FastqcData",
        "FastqcData-class"
      ]
    },
    {
      "page": "FastqcDataList",
      "title": "The FastqcDataList Object Class",
      "topics": [
        "FastqcDataList",
        "FastqcDataList-class"
      ]
    },
    {
      "page": "fqcVersion",
      "title": "Get the FASTQC version",
      "topics": [
        "fqcVersion",
        "fqcVersion,ANY-method",
        "fqcVersion,FastqcData-method",
        "fqcVersion,FastqcDataList-method"
      ]
    },
    {
      "page": "fqName-methods",
      "title": "Return the Underlying Fastq File Names from Fastqc/Fastp Objects",
      "topics": [
        "fqName",
        "fqName,ANY-method",
        "fqName,FastpData-method",
        "fqName,FastpDataList-method",
        "fqName,FastqcData-method",
        "fqName,FastqcDataList-method",
        "fqName<-",
        "fqName<-,FastqcData-method",
        "fqName<-,FastqcDataList-method"
      ]
    },
    {
      "page": "gcAvail",
      "title": "List Genomes or Transcriptomes with Theoretical GC Content",
      "topics": [
        "gcAvail",
        "gcAvail,TheoreticalGC-method"
      ]
    },
    {
      "page": "gcTheoretical",
      "title": "Theoretical GC content",
      "topics": [
        "gcTheoretical"
      ]
    },
    {
      "page": "getColours-methods",
      "title": "Work with objects of class PwfCols",
      "topics": [
        "getColours",
        "getColours,PwfCols-method",
        "setAlpha",
        "setAlpha,PwfCols-method",
        "setColours",
        "setColours,PwfCols-method"
      ]
    },
    {
      "page": "getGC",
      "title": "Get Theoretical GC content",
      "topics": [
        "getGC",
        "getGC,ANY-method",
        "getGC,TheoreticalGC-method"
      ]
    },
    {
      "page": "getModule",
      "title": "Retrieve a given module from a Fastqc* Object",
      "topics": [
        "getModule",
        "getModule,ANY-method",
        "getModule,FastpData-method",
        "getModule,FastpDataList-method",
        "getModule,FastqcData-method",
        "getModule,FastqcDataList-method"
      ]
    },
    {
      "page": "getSummary",
      "title": "Get the summary information from Fastqc Files",
      "topics": [
        "getSummary",
        "getSummary,.FastqcFile-method",
        "getSummary,ANY-method",
        "getSummary,FastqcData-method",
        "getSummary,FastqcDataList-method"
      ]
    },
    {
      "page": "importNgsLogs",
      "title": "Import Various NGS-related log files",
      "topics": [
        "importNgsLogs"
      ]
    },
    {
      "page": "importSJ",
      "title": "Import STAR Splice Junctions",
      "topics": [
        "importSJ"
      ]
    },
    {
      "page": "isCompressed",
      "title": "Check to see if a file is compressed",
      "topics": [
        "isCompressed"
      ]
    },
    {
      "page": "maxAdapterContent",
      "title": "Get the maximum Adapter Content",
      "topics": [
        "maxAdapterContent"
      ]
    },
    {
      "page": "mData",
      "title": "Extract Metadata for TheoreticalGC objects",
      "topics": [
        "mData",
        "mData,TheoreticalGC-method"
      ]
    },
    {
      "page": "overRep2Fasta-methods",
      "title": "Write fasta of Over-Represented sequences.",
      "topics": [
        "overRep2Fasta",
        "overRep2Fasta,ANY-method",
        "overRep2Fasta,FastqcData-method",
        "overRep2Fasta,FastqcDataList-method"
      ]
    },
    {
      "page": "path",
      "title": "Return the File Paths from an object",
      "topics": [
        "path",
        "path,.FastpFile-method",
        "path,.FastqcFile-method",
        "path,FastpData-method",
        "path,FastpDataList-method",
        "path,FastqcData-method",
        "path,FastqcDataList-method"
      ]
    },
    {
      "page": "plotAdapterContent-methods",
      "title": "Draw an Adapter Content Plot",
      "topics": [
        "plotAdapterContent",
        "plotAdapterContent,ANY-method",
        "plotAdapterContent,FastpData-method",
        "plotAdapterContent,FastpDataList-method",
        "plotAdapterContent,FastqcData-method",
        "plotAdapterContent,FastqcDataList-method"
      ]
    },
    {
      "page": "plotAlignmentSummary",
      "title": "Plot a summary of alignments",
      "topics": [
        "plotAlignmentSummary"
      ]
    },
    {
      "page": "plotAssemblyStats",
      "title": "Plot a summary of assembly logs",
      "topics": [
        "plotAssemblyStats"
      ]
    },
    {
      "page": "plotBaseQuals-methods",
      "title": "Plot the Base Qualities for each file",
      "topics": [
        "plotBaseQuals",
        "plotBaseQuals,ANY-method",
        "plotBaseQuals,FastpData-method",
        "plotBaseQuals,FastpDataList-method",
        "plotBaseQuals,FastqcData-method",
        "plotBaseQuals,FastqcDataList-method"
      ]
    },
    {
      "page": "plotDupLevels-methods",
      "title": "Plot the combined Sequence_Duplication_Levels information",
      "topics": [
        "plotDupLevels",
        "plotDupLevels,ANY-method",
        "plotDupLevels,FastpData-method",
        "plotDupLevels,FastpDataList-method",
        "plotDupLevels,FastqcData-method",
        "plotDupLevels,FastqcDataList-method"
      ]
    },
    {
      "page": "plotFastqcPCA-methods",
      "title": "Draw a PCA plot for Fast QC modules",
      "topics": [
        "plotFastqcPCA",
        "plotFastqcPCA,ANY-method",
        "plotFastqcPCA,character-method",
        "plotFastqcPCA,FastqcDataList-method"
      ]
    },
    {
      "page": "plotGcContent-methods",
      "title": "Plot the Per Sequence GC Content",
      "topics": [
        "plotGcContent",
        "plotGcContent,ANY-method",
        "plotGcContent,FastpData-method",
        "plotGcContent,FastpDataList-method",
        "plotGcContent,FastqcData-method",
        "plotGcContent,FastqcDataList-method"
      ]
    },
    {
      "page": "plotInsertSize-methods",
      "title": "Plot Insert Size Distributions",
      "topics": [
        "plotInsertSize",
        "plotInsertSize,FastpData-method",
        "plotInsertSize,FastpDataList-method"
      ]
    },
    {
      "page": "plotKmers-methods",
      "title": "Plot Overrepresented Kmers",
      "topics": [
        "plotKmers",
        "plotKmers,ANY-method",
        "plotKmers,FastpData-method",
        "plotKmers,FastqcData-method",
        "plotKmers,FastqcDataList-method"
      ]
    },
    {
      "page": "plotNContent-methods",
      "title": "Draw an N Content Plot",
      "topics": [
        "plotNContent",
        "plotNContent,ANY-method",
        "plotNContent,FastpData-method",
        "plotNContent,FastpDataList-method",
        "plotNContent,FastqcData-method",
        "plotNContent,FastqcDataList-method"
      ]
    },
    {
      "page": "plotOverrep-methods",
      "title": "Plot a summary of Over-represented Sequences",
      "topics": [
        "plotOverrep",
        "plotOverrep,ANY-method",
        "plotOverrep,character-method",
        "plotOverrep,FastqcData-method",
        "plotOverrep,FastqcDataList-method"
      ]
    },
    {
      "page": "plotReadTotals-methods",
      "title": "Draw a barplot of read totals",
      "topics": [
        "plotReadTotals",
        "plotReadTotals,ANY-method",
        "plotReadTotals,FastpDataList-method",
        "plotReadTotals,FastqcDataList-method"
      ]
    },
    {
      "page": "plotSeqContent-methods",
      "title": "Plot the per base content as a heatmap",
      "topics": [
        "plotSeqContent",
        "plotSeqContent,ANY-method",
        "plotSeqContent,FastpData-method",
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        "plotSeqContent,FastqcData-method",
        "plotSeqContent,FastqcDataList-method"
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    },
    {
      "page": "plotSeqLengthDistn-methods",
      "title": "Plot the Sequence Length Distribution",
      "topics": [
        "plotSeqLengthDistn",
        "plotSeqLengthDistn,ANY-method",
        "plotSeqLengthDistn,character-method",
        "plotSeqLengthDistn,FastqcData-method",
        "plotSeqLengthDistn,FastqcDataList-method"
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    },
    {
      "page": "plotSeqQuals-methods",
      "title": "Plot the Per Sequence Quality Scores",
      "topics": [
        "plotSeqQuals",
        "plotSeqQuals,ANY-method",
        "plotSeqQuals,character-method",
        "plotSeqQuals,FastqcData-method",
        "plotSeqQuals,FastqcDataList-method"
      ]
    },
    {
      "page": "plotSummary-methods",
      "title": "Plot the PASS/WARN/FAIL information",
      "topics": [
        "plotSummary",
        "plotSummary,ANY-method",
        "plotSummary,character-method",
        "plotSummary,FastqcDataList-method"
      ]
    },
    {
      "page": "pwf",
      "title": "Colours for PASS/WARN/FAIL",
      "topics": [
        "pwf"
      ]
    },
    {
      "page": "PwfCols-class",
      "title": "The PwfCols class and associated methods",
      "topics": [
        "PwfCols",
        "PwfCols-class"
      ]
    },
    {
      "page": "readTotals",
      "title": "Get the read totals",
      "topics": [
        "readTotals"
      ]
    },
    {
      "page": "summariseOverrep-methods",
      "title": "Summarise Overrepresented Sequences",
      "topics": [
        "summariseOverrep",
        "summariseOverrep,FastpData-method",
        "summariseOverrep,FastpDataList-method",
        "summariseOverrep,FastqcData-method",
        "summariseOverrep,FastqcDataList-method"
      ]
    },
    {
      "page": "TheoreticalGC-class",
      "title": "The TheoreticalGC Object Class",
      "topics": [
        "TheoreticalGC-class"
      ]
    },
    {
      "page": "writeHtmlReport",
      "title": "Write an HTML Summary Report",
      "topics": [
        "writeHtmlReport"
      ]
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  "_vignettes": [
    {
      "source": "ngsReportsIntroduction.Rmd",
      "filename": "ngsReportsIntroduction.html",
      "title": "An Introduction To ngsReports",
      "author": "Christopher Ward, Hien To, Stevie Pederson",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Basic Usage",
        "Using the Shiny App",
        "The default report",
        "Advanced Usage",
        "Classes Defined in the Package",
        "Loading FastQC Data Into R",
        "Generating Plots For One or More Fastqc Files",
        "Inspecting the PASS/WARN/FAIL Status of each module",
        "Visualising Read Totals",
        "Per Base Sequence Qualities",
        "Mean Sequence Quality Per Read",
        "Per Base Sequence Content",
        "Adapter Content",
        "Sequence Duplication Levels",
        "GC content",
        "The class TheoreticalGC",
        "Inspecting GC Content",
        "Overrepresented Sequences",
        "Importing Log Files",
        "Adapter removal and trimming",
        "Mapping and alignment",
        "Log file import",
        "Plot log file imports",
        "Genome assembly",
        "Session info"
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      "created": "2017-10-04 12:36:57",
      "modified": "2023-04-14 12:44:40",
      "commits": 51
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