{
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  "Package": "quaqcr",
  "Title": "Quick ATAC-Seq QC",
  "Version": "1.0.4.9000",
  "Authors@R": "person(c(\"Benjamin\", \"Jean-Marie\"), \"Tremblay\", role = c(\"aut\", \"cre\"),\nemail = \"benjmtremblay@gmail.com\",\ncomment = c(ORCID = \"0000-0002-7441-2951\"))",
  "Description": "A wrapper around the 'quaqc' program described in Tremblay\nand Questa (2024) <doi:10.1093/bioinformatics/btae649>. 'quaqc'\nallows for assay for transposase-accessible chromatin using\nsequencing (ATAC-seq) specific quality control and read\nfiltering of next-generation sequencing (NGS) data with minimal\nprocessing time and extremely low memory overhead. Any number\nof samples can be processed, using multiple threads if desired.\n'quaqc' outputs a comprehensive set of aligned read metrics,\nincluding alignment size, fragment size, percent duplicates,\nmapq scores, read depth, GC content, and others. Although\ndesigned for ATAC-seq data, 'quaqc' can also be used for other\nunspliced DNA sequencing experiments (such as chromatin\nimmunoprecipitation sequencing, or ChIP-seq) as many of the\nmetrics are related to general sequencing quality. This R\npackage also provides additional utilities for custom analyses\nand plotting of 'quaqc' results.",
  "URL": "https://github.com/bjmt/quaqcr",
  "BugReports": "https://github.com/bjmt/quaqcr/issues",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE, old_usage = TRUE)",
  "RoxygenNote": "7.3.3",
  "Config/testthat/edition": "3",
  "SystemRequirements": "quaqc (https://github.com/bjmt/quaqc)",
  "Repository": "https://bjmt.r-universe.dev",
  "Date/Publication": "2026-05-24 09:50:20 UTC",
  "RemoteUrl": "https://github.com/bjmt/quaqcr",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-06 09:00:38 UTC",
    "User": "root"
  },
  "Author": "Benjamin Jean-Marie Tremblay [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-7441-2951>)",
  "Maintainer": "Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>",
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  "_created": "2026-10-06T09:00:38.000Z",
  "_published": "2026-10-06T09:04:46.169Z",
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    "author": "Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>",
    "committer": "Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>",
    "message": "add helpers to read quaqc output files\n\nread_bedgraph(), read_bed(), read_narrowpeak(), read_qscore(), and\nread_quant() take a quaqc/quaqc_report object and load the corresponding\noutput files. Paths are derived from each sample's BAM filename with\noptional dir/ext overrides matching the quaqc() arguments. The filtered\nBAM (--keep) output is intentionally excluded.\n",
    "time": 1779616220
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  "_updates": [
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      "n": 5
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      "date": "2026-05-05"
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      "date": "2026-05-07"
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      "date": "2026-05-09"
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      "date": "2026-05-22"
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/quaqcr"
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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    "extra/NEWS.html",
    "extra/NEWS.txt",
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    "extra/readme.html",
    "extra/readme.md"
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  "_exports": [
    "footprint",
    "melt_reports",
    "parse_quaqc",
    "parse_quaqc_file",
    "pileup",
    "quaqc",
    "read_bed",
    "read_bedgraph",
    "read_narrowpeak",
    "read_qscore",
    "read_quant"
  ],
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    {
      "page": "footprint",
      "title": "Get transcription factor footprints with quaqc.",
      "topics": [
        "footprint"
      ]
    },
    {
      "page": "melt_reports",
      "title": "Melt sections of a quaqc report into a data.frame.",
      "topics": [
        "melt_reports"
      ]
    },
    {
      "page": "parse_quaqc",
      "title": "Parse a JSON quaqc report file.",
      "topics": [
        "parse_quaqc",
        "parse_quaqc_file"
      ]
    },
    {
      "page": "pileup",
      "title": "Generate read pileups from BAMs with quaqc.",
      "topics": [
        "pileup"
      ]
    },
    {
      "page": "quaqc",
      "title": "Run quaqc from within R.",
      "topics": [
        "quaqc"
      ]
    },
    {
      "page": "quaqcr-pkg",
      "title": "quaqcr: Quick ATAC-seq QC in R",
      "topics": [
        "quaqcr-package",
        "quaqcr",
        "quaqcr-pkg"
      ]
    },
    {
      "page": "read_quaqc_output",
      "title": "Read quaqc output files associated with a report.",
      "topics": [
        "read_bed",
        "read_bedgraph",
        "read_narrowpeak",
        "read_qscore",
        "read_quant",
        "read_quaqc_output"
      ]
    }
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