{
  "_id": "6a1e93a51d7bb097a0a6afb9",
  "Package": "Anaquin",
  "Type": "Package",
  "Title": "Statistical analysis of sequins",
  "Version": "2.36.0",
  "Date": "2017-08-08",
  "Author": "Ted Wong",
  "Maintainer": "Ted Wong <t.wong@garvan.org.au>",
  "Description": "The project is intended to support the use of sequins\n(synthetic sequencing spike-in controls) owned and made\navailable by the Garvan Institute of Medical Research. The goal\nis to provide a standard open source library for quantitative\nanalysis, modelling and visualization of spike-in controls.",
  "License": "BSD_3_clause + file LICENSE",
  "VignetteBuilder": "knitr",
  "URL": "www.sequin.xyz",
  "BugReports": "https://github.com/student-t/RAnaquin/issues",
  "LazyData": "true",
  "biocViews": "ImmunoOncology, DifferentialExpression, Preprocessing,\nRNASeq, GeneExpression, Software",
  "Config/pak/sysreqs": "libicu-dev zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:44:04 UTC",
  "RemoteUrl": "https://github.com/bioc/Anaquin",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "f4980d78dab8a4721718a768ee18a991fe308c5a",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-02 08:21:51 UTC",
    "User": "root"
  },
  "MD5sum": "309e9a81ea1592597d4274416b0e78e1",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "Anaquin_2.36.0.tar.gz",
  "_fileid": "51109f06ed99062fe13b174db831ef9ee8973ed62c232e2c73a7ac1f216bc898",
  "_filesize": 1102954,
  "_sha256": "51109f06ed99062fe13b174db831ef9ee8973ed62c232e2c73a7ac1f216bc898",
  "_created": "2026-06-02T08:21:51.000Z",
  "_published": "2026-06-02T08:26:13.377Z",
  "_jobs": [
    {
      "job": 79029226736,
      "time": 170,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7352625187"
    },
    {
      "job": 79029226353,
      "time": 226,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7352644888"
    },
    {
      "job": 79029226271,
      "time": 224,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7352643883"
    },
    {
      "job": 79029226320,
      "time": 98,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7352602466"
    },
    {
      "job": 79029226277,
      "time": 153,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7352619573"
    },
    {
      "job": 79028570813,
      "time": 239,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7352568503"
    },
    {
      "job": 79029226263,
      "time": 149,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7352617164"
    },
    {
      "job": 79029226306,
      "time": 158,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7352621530"
    },
    {
      "job": 79029226275,
      "time": 118,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7352607904"
    },
    {
      "job": 79029226257,
      "time": 133,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7352612776"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 0,
    "note": 15
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807452621",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/Anaquin",
  "_commit": {
    "id": "f4980d78dab8a4721718a768ee18a991fe308c5a",
    "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": 1777380244
  },
  "_maintainer": {
    "name": "Ted Wong",
    "email": "t.wong@garvan.org.au",
    "login": "garvanbio",
    "description": "",
    "uuid": 142758693
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.3",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "version": ">= 2.2.0",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ROCR",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Imports"
    },
    {
      "package": "qvalue",
      "role": "Imports"
    },
    {
      "package": "locfit",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "DESeq2",
      "role": "Imports"
    },
    {
      "package": "RUnit",
      "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": "2.37.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.36.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "differentialexpression",
    "preprocessing",
    "rnaseq",
    "geneexpression",
    "software"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 390,
    "source": "https://www.bioconductor.org/packages/stats/bioc/Anaquin"
  },
  "_searchresults": 49,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/Anaquin.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "plotConjoint",
    "plotLinear",
    "plotLOD",
    "plotLogistic",
    "plotROC"
  ],
  "_datasets": [
    {
      "name": "RnaQuinGeneMixture",
      "title": "RnaQuin mixture (gene level)",
      "object": "RnaQuinGeneMixture",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Name",
        "Length",
        "MixA",
        "MixB"
      ],
      "rows": 78,
      "table": true,
      "tojson": true
    },
    {
      "name": "RnaQuinIsoformMixture",
      "title": "RnaQuin mixture (isoform level)",
      "object": "RnaQuinIsoformMixture",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Name",
        "Length",
        "MixA",
        "MixB"
      ],
      "rows": 164,
      "table": true,
      "tojson": true
    },
    {
      "name": "UserGuideData_5.4.5.1",
      "title": "Section 5.4.5.1 Assembly Dataset",
      "object": "UserGuideData_5.4.5.1",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Input",
        "Sn"
      ],
      "rows": 164,
      "table": true,
      "tojson": true
    },
    {
      "name": "UserGuideData_5.4.6.3",
      "title": "Gene expression (RnaQuin)",
      "object": "UserGuideData_5.4.6.3",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Input",
        "Observed1",
        "Observed2",
        "Observed3"
      ],
      "rows": 73,
      "table": true,
      "tojson": true
    },
    {
      "name": "UserGuideData_5.6.3",
      "title": "Differential expression (RnaQuin)",
      "object": "UserGuideData_5.6.3",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ExpLFC",
        "ObsLFC",
        "SD",
        "Pval",
        "Qval",
        "Mean",
        "Label"
      ],
      "rows": 78,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "plotConjoint",
      "title": "Create conjoint plots",
      "topics": [
        "plotConjoint"
      ]
    },
    {
      "page": "plotLinear",
      "title": "Plot linear model for sequins",
      "topics": [
        "plotLinear"
      ]
    },
    {
      "page": "plotLOD",
      "title": "Create Limit-of-Detection Ratio (LOD) plot",
      "topics": [
        "plotLOD"
      ]
    },
    {
      "page": "plotLogistic",
      "title": "Plot logistic model for sequins",
      "topics": [
        "plotLogistic"
      ]
    },
    {
      "page": "plotROC",
      "title": "Create ROC plot",
      "topics": [
        "plotROC"
      ]
    },
    {
      "page": "RnaQuinGeneMixture",
      "title": "RnaQuin mixture (gene level)",
      "topics": [
        "RnaQuinGeneMixture"
      ]
    },
    {
      "page": "RnaQuinIsoformMixture",
      "title": "RnaQuin mixture (isoform level)",
      "topics": [
        "RnaQuinIsoformMixture"
      ]
    },
    {
      "page": "UserGuideData_5.4.5.1",
      "title": "Section 5.4.5.1 Assembly Dataset",
      "topics": [
        "UserGuideData_5.4.5.1"
      ]
    },
    {
      "page": "UserGuideData_5.4.6.3",
      "title": "Gene expression (RnaQuin)",
      "topics": [
        "UserGuideData_5.4.6.3"
      ]
    },
    {
      "page": "UserGuideData_5.6.3",
      "title": "Differential expression (RnaQuin)",
      "topics": [
        "UserGuideData_5.6.3"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/Anaquin/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "bitops",
    "caTools",
    "cli",
    "codetools",
    "cpp11",
    "DelayedArray",
    "DESeq2",
    "evaluate",
    "farver",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gplots",
    "gtable",
    "gtools",
    "highr",
    "IRanges",
    "isoband",
    "KernSmooth",
    "knitr",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "locfit",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "plyr",
    "qvalue",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "reshape2",
    "rlang",
    "ROCR",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "Anaquin.Rmd",
      "filename": "Anaquin.html",
      "title": "Anaquin - Vignette",
      "author": "Ted Wong (t.wong@garvan.org.au)",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Citation",
        "Website",
        "Overview",
        "Sequins",
        "Mixture",
        "Quantifying transcriptome assembly",
        "Quantifying gene expression",
        "Differential analysis"
      ],
      "created": "2016-08-26 19:47:20",
      "modified": "2017-08-08 05:12:47",
      "commits": 8
    }
  ],
  "_score": 4.690196080028514,
  "_indexed": false,
  "_nocasepkg": "anaquin",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/Anaquin",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.36.0",
      "date": "2026-06-02T08:25:08.000Z",
      "distro": "noble",
      "commit": "f4980d78dab8a4721718a768ee18a991fe308c5a",
      "fileid": "84a2d2500ebe1de05cdf47f6671349be3c54cca6fd2cffb3d4590b7f0f57096b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807452621"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.36.0",
      "date": "2026-06-02T08:25:16.000Z",
      "distro": "noble",
      "commit": "f4980d78dab8a4721718a768ee18a991fe308c5a",
      "fileid": "866cc224a143f224677c37d4193d0533cb5635026f2210aa5e8f30aebc5cc5c1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807452621"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.36.0",
      "date": "2026-06-02T08:23:26.000Z",
      "commit": "f4980d78dab8a4721718a768ee18a991fe308c5a",
      "fileid": "b9c02e834685f6ff3087662964c9dd53e5c553fd8f67a4b70aec8d19f4959c01",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807452621"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.36.0",
      "date": "2026-06-02T08:23:47.000Z",
      "commit": "f4980d78dab8a4721718a768ee18a991fe308c5a",
      "fileid": "c0f2fff7c5d525bd5470e82f3abf49b54367dd863d9ad0e92c8bfb19d266c9bc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807452621"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.36.0",
      "date": "2026-06-02T08:24:33.000Z",
      "commit": "f4980d78dab8a4721718a768ee18a991fe308c5a",
      "fileid": "bfaf9693e9a9ea681ebbea4ed7b8461327905d68f85bd26bff59e20ecf964c17",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807452621"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.36.0",
      "date": "2026-06-02T08:24:06.000Z",
      "commit": "f4980d78dab8a4721718a768ee18a991fe308c5a",
      "fileid": "6b5e314dae108c772627247de25d16ccb7eaeffd32b045c36babddaf04687383",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807452621"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.36.0",
      "date": "2026-06-02T08:23:19.000Z",
      "commit": "f4980d78dab8a4721718a768ee18a991fe308c5a",
      "fileid": "001542ed4a885ac8267c1bd6abec0eefbc7f10b681803257d12ee30a37c68a13",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807452621"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.36.0",
      "date": "2026-06-02T08:23:30.000Z",
      "commit": "f4980d78dab8a4721718a768ee18a991fe308c5a",
      "fileid": "0daf6ef7a91e2e2410baaae036a011b744add536089ec5af135a9947de03a8ef",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807452621"
    }
  ]
}