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  "Package": "IONiseR",
  "Title": "Quality Assessment Tools for Oxford Nanopore MinION data",
  "Version": "2.13.1",
  "Authors@R": "person(\"Mike\", \"Smith\", email = \"grimbough@gmail.com\", role\n= c(\"aut\", \"cre\"))",
  "Description": "IONiseR provides tools for the quality assessment of\nOxford Nanopore MinION data. It extracts summary statistics\nfrom a set of fast5 files and can be used either before or\nafter base calling.  In addition to standard summaries of the\nread-types produced, it provides a number of plots for\nvisualising metrics relative to experiment run time or\nspatially over the surface of a flowcell.",
  "License": "MIT + file LICENSE",
  "VignetteBuilder": "knitr",
  "biocViews": "QualityControl, DataImport, Sequencing",
  "NeedsCompilation": "no",
  "Author": "Mike Smith [aut, cre]",
  "Maintainer": "Mike Smith <grimbough@gmail.com>",
  "RoxygenNote": "6.0.1",
  "Collate": "'IONiseR.R' 'classes.R' 'Methods-accessors.R'\n'Methods-subsetting.R' 'fast5Readers.R' 'fast5Status.R'\n'fast5readers_summary.R' 'fast5utilities.R' 'fastqProcessing.R'\n'plotting_kmers.R' 'plotting_layout.R'\n'plotting_summaryStats.R' 'processing_bam.R' 'readSummary.R'\n'squiggle.R'",
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  "Repository": "https://grimbough.r-universe.dev",
  "Date/Publication": "2020-09-21 15:33:30 UTC",
  "RemoteUrl": "https://github.com/grimbough/IONiseR",
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  "_published": "2026-10-07T11:55:09.725Z",
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    "extra/citation.json",
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    "channelActivityPlot",
    "channelHeatmap",
    "eventData",
    "fast5toFastq",
    "fastq",
    "fastq2D",
    "fastqComplement",
    "fastqTemplate",
    "layoutPlot",
    "plotActiveChannels",
    "plotBaseProductionRate",
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    "plotEventRate",
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    "plotReadAccumulation",
    "plotReadCategoryCounts",
    "plotReadCategoryQuals",
    "plotReadTypeProduction",
    "readFast5Log",
    "readFast5Summary",
    "readInfo"
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    {
      "page": "baseCalled",
      "title": "Extract baseCalled slot",
      "topics": [
        "baseCalled"
      ]
    },
    {
      "page": "channelActivityPlot",
      "title": "Visualise a specified metric over all channels over time.",
      "topics": [
        "channelActivityPlot"
      ]
    },
    {
      "page": "channelHeatmap",
      "title": "Create layout plot of flowcell",
      "topics": [
        "channelHeatmap"
      ]
    },
    {
      "page": "eventData",
      "title": "Extract eventData slot",
      "topics": [
        "eventData"
      ]
    },
    {
      "page": "Fast5Summary-class",
      "title": "An S4 class for summarised data from a MinION sequencing run",
      "topics": [
        "baseCalled,Fast5Summary-method",
        "eventData,Fast5Summary-method",
        "Fast5Summary-class",
        "fastq,Fast5Summary-method",
        "fastq2D,Fast5Summary-method",
        "fastqComplement,Fast5Summary-method",
        "fastqTemplate,Fast5Summary-method",
        "length,Fast5Summary-method",
        "readInfo,Fast5Summary-method",
        "[,Fast5Summary,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "fast5toFastq",
      "title": "Extract FASTQ files from fast5 files",
      "topics": [
        "fast5toFastq"
      ]
    },
    {
      "page": "fastq",
      "title": "Extract fastq slot",
      "topics": [
        "fastq"
      ]
    },
    {
      "page": "fastq2D",
      "title": "Extract 2D reads",
      "topics": [
        "fastq2D"
      ]
    },
    {
      "page": "fastqComplement",
      "title": "Extract complement reads",
      "topics": [
        "fastqComplement"
      ]
    },
    {
      "page": "fastqTemplate",
      "title": "Extract template reads",
      "topics": [
        "fastqTemplate"
      ]
    },
    {
      "page": "IONiseR",
      "title": "IONiseR: A package for assessing quality of MinION data",
      "topics": [
        "IONiseR-package",
        "IONiseR"
      ]
    },
    {
      "page": "layoutPlot",
      "title": "Create layout plot of flowcell",
      "topics": [
        "layoutPlot"
      ]
    },
    {
      "page": "muxHeatmap",
      "title": "Create layout plot of flowcell",
      "topics": [
        "muxHeatmap"
      ]
    },
    {
      "page": "plotActiveChannels",
      "title": "Plot the number of active channels for each minute of run time",
      "topics": [
        "plotActiveChannels"
      ]
    },
    {
      "page": "plotBaseProductionRate",
      "title": "Plot the mean rate at which bases are recorded",
      "topics": [
        "plotBaseProductionRate"
      ]
    },
    {
      "page": "plotCurrentByTime",
      "title": "View changes in signal against run time.",
      "topics": [
        "plotCurrentByTime"
      ]
    },
    {
      "page": "plotEventRate",
      "title": "Plot the mean rate at which events occur",
      "topics": [
        "plotEventRate"
      ]
    },
    {
      "page": "plotKmerFrequencyCorrelation",
      "title": "Display correlation between pentemer proportions in two time windows",
      "topics": [
        "plotKmerFrequencyCorrelation"
      ]
    },
    {
      "page": "plotReadAccumulation",
      "title": "Plot the accumulation of reads over the duration of the experiment.",
      "topics": [
        "plotReadAccumulation"
      ]
    },
    {
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      "title": "Plot the proportion of template, complement and 2D reads found a dataset.",
      "topics": [
        "plotReadCategoryCounts"
      ]
    },
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        "plotReadCategoryQuals"
      ]
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      "page": "plotReadTypeProduction",
      "title": "View changes in signal against run time.",
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        "plotReadTypeProduction"
      ]
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      ]
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      "page": "readFast5Summary",
      "title": "Read summary data from fast5 files.",
      "topics": [
        "readFast5Summary"
      ]
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      "title": "Extract readInfo slot",
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        "readInfo"
      ]
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