{
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  "Package": "basecallQC",
  "Type": "Package",
  "Title": "Working with Illumina Basecalling and Demultiplexing input and\noutput files",
  "Version": "1.36.0",
  "Author": "Thomas Carroll and Marian Dore",
  "Maintainer": "Thomas Carroll <tc.infomatics@gmail.com>",
  "Description": "The basecallQC package provides tools to work with\nIllumina bcl2Fastq (versions >= 2.1.7) software.Prior to\nbasecalling and demultiplexing using the bcl2Fastq software,\nbasecallQC functions allow the user to update Illumina sample\nsheets from versions <= 1.8.9 to >= 2.1.7 standards, clean\nsample sheets of common problems such as invalid sample names\nand IDs, create read and index basemasks and the bcl2Fastq\ncommand. Following the generation of basecalled and\ndemultiplexed data, the basecallQC packages allows the user to\ngenerate HTML tables, plots and a self contained report of\nsummary metrics from Illumina XML output files.",
  "biocViews": "Sequencing, Infrastructure, DataImport, QualityControl",
  "License": "GPL (>= 3)",
  "VignetteBuilder": "knitr",
  "SystemRequirements": "bcl2Fastq (versions >= 2.1.7)",
  "Collate": "processIlluminaSamplesheets_Functions.R\nprocessXMLs_Functions.R allClasses.R allMethods.R\nprocessExternalFormats_Functions.R plots.R reporting.R tables.R\nFastQCShortRead_Functions.R processInterOps_Functions.R zzz.R",
  "RoxygenNote": "7.1.0",
  "PackageStatus": "Deprecated",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:45:29 UTC",
  "RemoteUrl": "https://github.com/bioc/basecallQC",
  "RemoteRef": "RELEASE_3_23",
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  "_selfowned": false,
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  "_userbio": {
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    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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      "page": "baseCallMetrics",
      "title": "Gather basecalling metrics from a Run (using Run's ConversionStats.xml file).",
      "topics": [
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      ]
    },
    {
      "page": "basecallQC",
      "title": "The basecallQC object and constructor.",
      "topics": [
        "basecallQC",
        "basecallQC-basecallQC",
        "basecallQC-class"
      ]
    },
    {
      "page": "BCL2FastQparams",
      "title": "The Parameters for BCL2FastQparams object.",
      "topics": [
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        "BCL2FastQparams-BCL2FastQparams",
        "BCL2FastQparams-class"
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    },
    {
      "page": "createBasemasks",
      "title": "Function to create basemasks for basecalling from Illumina samplesheet (for bcl2Fastq versions >= 2.1.7).",
      "topics": [
        "createBasemasks"
      ]
    },
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      "title": "Function to create command for Illumina basecalling/demultiplexing using bcl2fastq versions >= 2.1.7.",
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      ]
    },
    {
      "page": "demultiplexMetrics",
      "title": "Gather demultiplexing metrics from a Run (using Run's DemultiplexingStats.xml file).",
      "topics": [
        "demultiplexMetrics"
      ]
    },
    {
      "page": "demuxBarplot",
      "title": "Barplot of Illumina demultiplexing statistics.",
      "topics": [
        "demuxBarplot",
        "demuxBarplot,baseCallQC-method",
        "demuxBarplot,basecallQC-method",
        "demuxBarplot,list-method",
        "demuxBarplot.basecallQC"
      ]
    },
    {
      "page": "demuxBoxplot",
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        "demuxBoxplot,baseCallQC-method",
        "demuxBoxplot,basecallQC-method",
        "demuxBoxplot,list-method",
        "demuxBoxplot.basecallQC"
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    },
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        "indexlengths,BCL2FastQparams-method",
        "indexlengths,BCL2FastQparams-method,",
        "indexlengths.bcl2fastqparams"
      ]
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      "topics": [
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      ]
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      "topics": [
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      ]
    },
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      "title": "Barplot of Illumina basecalling statistics for reads passing filter.",
      "topics": [
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        "passFilterBar,baseCallQC-method",
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        "passFilterBar,list-method",
        "passFilterBar.basecallQC"
      ]
    },
    {
      "page": "passFilterBoxplot",
      "title": "Boxplot of Illumina basecalling statistics for reads passing filter.",
      "topics": [
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        "passFilterBoxplot,baseCallQC-method",
        "passFilterBoxplot,basecallQC-method",
        "passFilterBoxplot,list-method",
        "passFilterBoxplot.basecallQC"
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      "topics": [
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        "passFilterTilePlot,baseCallQC-method",
        "passFilterTilePlot,basecallQC-method",
        "passFilterTilePlot,list-method",
        "passFilterTilePlot.basecallQC"
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        "reportBCL,basecallQC-method",
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      ]
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