{
  "_id": "6a2d0ed23efcd9bda42f0242",
  "Package": "miQC",
  "Type": "Package",
  "Title": "Flexible, probabilistic metrics for quality control of scRNA-seq\ndata",
  "Version": "1.20.0",
  "Authors@R": "c(person(\"Ariel\", \"Hippen\", role = c(\"aut\", \"cre\"),\nemail = \"ariel.hippen@gmail.com\"),\nperson(\"Stephanie\", \"Hicks\", role = c(\"aut\"),\nemail = \"shicks19@jhu.edu\"))",
  "Description": "Single-cell RNA-sequencing (scRNA-seq) has made it\npossible to profile gene expression in tissues at high\nresolution.  An important preprocessing step prior to\nperforming downstream analyses is to identify and remove cells\nwith poor or degraded sample quality using quality control (QC)\nmetrics.  Two widely used QC metrics to identify a\n‘low-quality’ cell are (i) if the cell includes a high\nproportion of reads that map to mitochondrial DNA encoded genes\n(mtDNA) and (ii) if a small number of genes are detected. miQC\nis data-driven QC metric that jointly models both the\nproportion of reads mapping to mtDNA and the number of detected\ngenes with mixture models in a probabilistic framework to\npredict the low-quality cells in a given dataset.",
  "URL": "https://github.com/greenelab/miQC",
  "BugReports": "https://github.com/greenelab/miQC/issues",
  "License": "BSD_3_clause + file LICENSE",
  "biocViews": "SingleCell, QualityControl, GeneExpression, Preprocessing,\nSequencing",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.2.1",
  "LazyData": "TRUE",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:55:11 UTC",
  "RemoteUrl": "https://github.com/bioc/miQC",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "cec28aef59e90b34cdddcd8ec886c87ecfcd84f8",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-13 07:36:26 UTC",
    "User": "root"
  },
  "Author": "Ariel Hippen [aut, cre],\nStephanie Hicks [aut]",
  "Maintainer": "Ariel Hippen <ariel.hippen@gmail.com>",
  "MD5sum": "5be6d233e8dd6e668142cb4b7ba1fb1c",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "miQC_1.20.0.tar.gz",
  "_fileid": "bbafe35702c908e13a96960d1a99614bb1f59e626ab395f3a349df8ae586a384",
  "_filesize": 2518426,
  "_sha256": "bbafe35702c908e13a96960d1a99614bb1f59e626ab395f3a349df8ae586a384",
  "_created": "2026-06-13T07:36:26.000Z",
  "_published": "2026-06-13T08:03:30.674Z",
  "_jobs": [
    {
      "job": 81173390612,
      "time": 244,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7608729315"
    },
    {
      "job": 81173390611,
      "time": 384,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7608745765"
    },
    {
      "job": 81173390622,
      "time": 409,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7608748949"
    },
    {
      "job": 81173390615,
      "time": 208,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7608723747"
    },
    {
      "job": 81173390623,
      "time": 272,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7608731948"
    },
    {
      "job": 81173026511,
      "time": 347,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7608696381"
    },
    {
      "job": 81173390616,
      "time": 204,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7608724211"
    },
    {
      "job": 81173390618,
      "time": 1310,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7608859738"
    },
    {
      "job": 81173390632,
      "time": 1423,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7608873091"
    },
    {
      "job": 81173390619,
      "time": 1570,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7608892211"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 8
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27460417300",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/miQC",
  "_commit": {
    "id": "cec28aef59e90b34cdddcd8ec886c87ecfcd84f8",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777380911
  },
  "_maintainer": {
    "name": "Ariel Hippen",
    "email": "ariel.hippen@gmail.com",
    "login": "arielah",
    "linkedin": "in/arielhippen",
    "description": "Computational biologist interested in finding and designing the best tools to understand and cure disease. Currently active in private account through employer.",
    "uuid": 14189222
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "flexmix",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "splines",
      "role": "Imports"
    },
    {
      "package": "scRNAseq",
      "role": "Suggests"
    },
    {
      "package": "scater",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.21.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.20.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "singlecell",
    "qualitycontrol",
    "geneexpression",
    "preprocessing",
    "sequencing"
  ],
  "_stars": 22,
  "_contributors": [
    {
      "user": "arielah",
      "count": 36,
      "uuid": 14189222
    },
    {
      "user": "nturaga",
      "count": 6,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 2,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 429,
    "source": "https://www.bioconductor.org/packages/stats/bioc/miQC"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/greenelab/miqc",
  "_searchresults": 112,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/miQC.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/greenelab/miqc",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "filterCells",
    "get1DCutoff",
    "mixtureModel",
    "plotFiltering",
    "plotMetrics",
    "plotModel"
  ],
  "_datasets": [
    {
      "name": "metrics",
      "title": "Basic scRNA-seq QC metrics from an ovarian tumor",
      "object": "hgsoc_metrics",
      "class": [
        "DFrame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "filterCells",
      "title": "filterCells",
      "topics": [
        "filterCells"
      ]
    },
    {
      "page": "get1DCutoff",
      "title": "get1DCutoff",
      "topics": [
        "get1DCutoff"
      ]
    },
    {
      "page": "metrics",
      "title": "Basic scRNA-seq QC metrics from an ovarian tumor",
      "topics": [
        "metrics"
      ]
    },
    {
      "page": "mixtureModel",
      "title": "mixtureModel",
      "topics": [
        "mixtureModel"
      ]
    },
    {
      "page": "plotFiltering",
      "title": "plotFiltering",
      "topics": [
        "plotFiltering"
      ]
    },
    {
      "page": "plotMetrics",
      "title": "plotMetrics",
      "topics": [
        "plotMetrics"
      ]
    },
    {
      "page": "plotModel",
      "title": "plotModel",
      "topics": [
        "plotModel"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/miQC/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "Biobase",
    "BiocGenerics",
    "cli",
    "cpp11",
    "DelayedArray",
    "farver",
    "flexmix",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "IRanges",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "modeltools",
    "nnet",
    "R6",
    "RColorBrewer",
    "rlang",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "SingleCellExperiment",
    "SparseArray",
    "SummarizedExperiment",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "miQC.Rmd",
      "filename": "miQC.html",
      "title": "An introduction to miQC",
      "author": "Ariel Hippen and Stephanie Hicks",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Introduction",
        "Example data",
        "Scater preprocessing",
        "miQC",
        "Basic usage",
        "Other model types",
        "Extras",
        "Changing posterior cutoff",
        "Preventing exclusion of low-mito cells",
        "Preventing U-shaped boundary",
        "When not to use miQC",
        "Session Information",
        "References"
      ],
      "created": "2021-02-25 19:27:05",
      "modified": "2023-01-04 16:13:16",
      "commits": 6
    }
  ],
  "_score": 6.692670699156369,
  "_indexed": false,
  "_nocasepkg": "miqc",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/miQC",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.20.0",
      "date": "2026-06-13T07:40:33.000Z",
      "distro": "noble",
      "commit": "cec28aef59e90b34cdddcd8ec886c87ecfcd84f8",
      "fileid": "5bfa794ce0d59a7e8cd1ea9516ecc0bf059259727161fb76d1878691669177b4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27460417300"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.20.0",
      "date": "2026-06-13T07:41:12.000Z",
      "distro": "noble",
      "commit": "cec28aef59e90b34cdddcd8ec886c87ecfcd84f8",
      "fileid": "f11651bfdc9a2b7491eff1f6185d3d7b33d53512d9ee5e28376dec28c91875c9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27460417300"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.20.0",
      "date": "2026-06-13T07:38:37.000Z",
      "commit": "cec28aef59e90b34cdddcd8ec886c87ecfcd84f8",
      "fileid": "0b66986be4c34b8046debc0d041a50453922d8a1b373ebe36829727e88e7b2d5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27460417300"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.20.0",
      "date": "2026-06-13T07:39:24.000Z",
      "commit": "cec28aef59e90b34cdddcd8ec886c87ecfcd84f8",
      "fileid": "e978ca0481f354c111c3a51915cda561728267392f25daad2ac58ef13a0fda61",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27460417300"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.20.0",
      "date": "2026-06-13T07:40:23.000Z",
      "commit": "cec28aef59e90b34cdddcd8ec886c87ecfcd84f8",
      "fileid": "531f27c2c1cc678ce30cc75b468fb6474b3554813a7cc3887e3e4c6de049d779",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27460417300"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.20.0",
      "date": "2026-06-13T07:56:17.000Z",
      "commit": "cec28aef59e90b34cdddcd8ec886c87ecfcd84f8",
      "fileid": "fef1857697c5776197a5e53b20898f7bfac0516957237e0cbed3ce6fe4805f6c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27460417300"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.20.0",
      "date": "2026-06-13T07:57:56.000Z",
      "commit": "cec28aef59e90b34cdddcd8ec886c87ecfcd84f8",
      "fileid": "8ba3ea5e3e15f62d31bf91fb57c13ba2a709cbc3501baaa95cb3d119c24eee30",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27460417300"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.20.0",
      "date": "2026-06-13T08:00:21.000Z",
      "commit": "cec28aef59e90b34cdddcd8ec886c87ecfcd84f8",
      "fileid": "831b8954d1e4a573c9ce1d864244744f8a4075a61af8fd57678a143efe68f2ca",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27460417300"
    }
  ]
}