{
  "_id": "6a21591ccd65a98ecbd2ec20",
  "Package": "denoiSeq",
  "Type": "Package",
  "Title": "Differential Expression Analysis Using a Bottom-Up Model",
  "Version": "0.1.1",
  "Authors@R": "c(person(\"Gershom\", \"Buri\", email = \"buri@aims.edu.gh\", role = c(\"aut\",\"cre\")),person(\"Wilfred\", \"Ndifon\", email = \"ndifon@gmail.com\", role = \"aut\"))",
  "Description": "Given count data from two conditions, it determines which\ntranscripts are differentially expressed across the two\nconditions using Bayesian inference of the parameters of a\nbottom-up model for PCR amplification. This model is developed\nin Ndifon Wilfred, Hilah Gal, Eric Shifrut, Rina Aharoni,\nNissan Yissachar, Nir Waysbort, Shlomit Reich Zeliger, Ruth\nArnon, and Nir Friedman (2012),\n<http://www.pnas.org/content/109/39/15865.full>, and results in\na distribution for the counts that is a superposition of the\nbinomial and negative binomial distribution.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "6.0.1",
  "VignetteBuilder": "knitr, rmarkdown",
  "Repository": "https://buriom.r-universe.dev",
  "Date/Publication": "2018-01-22 15:00:29 UTC",
  "RemoteUrl": "https://github.com/buriom/denoiseq",
  "RemoteRef": "HEAD",
  "RemoteSha": "96e629965741d4cf90bfe03722d3d004d4990a9b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-04 10:49:01 UTC",
    "User": "root"
  },
  "Author": "Gershom Buri [aut, cre],\nWilfred Ndifon [aut]",
  "Maintainer": "Gershom Buri <buri@aims.edu.gh>",
  "MD5sum": "bc65ae005b9ca376b437db72a8e9985f",
  "_user": "buriom",
  "_type": "src",
  "_file": "denoiSeq_0.1.1.tar.gz",
  "_fileid": "92882a53b25ab9ef376e2a11786e15a39c3a60738faa3f3134354925699cf3d4",
  "_filesize": 280824,
  "_sha256": "92882a53b25ab9ef376e2a11786e15a39c3a60738faa3f3134354925699cf3d4",
  "_created": "2026-06-04T10:49:01.000Z",
  "_published": "2026-06-04T10:53:16.167Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79502760399,
      "time": 139,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7409549275"
    },
    {
      "job": 79502760383,
      "time": 127,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7409545634"
    },
    {
      "job": 79502760408,
      "time": 146,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7409545120"
    },
    {
      "job": 79502760407,
      "time": 160,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7409547784"
    },
    {
      "job": 79502304230,
      "time": 178,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7409504700"
    },
    {
      "job": 79502760384,
      "time": 104,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7409538036"
    },
    {
      "job": 79502760435,
      "time": 219,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7409574474"
    },
    {
      "job": 79502760411,
      "time": 83,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7409530549"
    },
    {
      "job": 79502760455,
      "time": 103,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7409538129"
    }
  ],
  "_buildurl": "https://github.com/r-universe/buriom/actions/runs/26946974774",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/buriom/denoiseq",
  "_commit": {
    "id": "96e629965741d4cf90bfe03722d3d004d4990a9b",
    "author": "buri <buri@aims.edu.gh>",
    "committer": "buri <buri@aims.edu.gh>",
    "message": "fixed the methods' documentation\n",
    "time": 1516633229
  },
  "_maintainer": {
    "name": "Gershom Buri",
    "email": "buri@aims.edu.gh",
    "login": "buriom",
    "description": "",
    "uuid": 6714317
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "buriom",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "buriom",
      "count": 25,
      "uuid": 6714317
    }
  ],
  "_userbio": {
    "uuid": 6714317,
    "type": "user",
    "name": "Gershom Buri"
  },
  "_downloads": {
    "count": 152,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/denoiSeq"
  },
  "_devurl": "https://github.com/buriom/denoiseq",
  "_searchresults": 10,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/denoiSeq.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/buriom/denoiseq",
  "_realowner": "buriom",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2017-07-18"
    },
    {
      "version": "0.1.1",
      "date": "2018-01-31"
    }
  ],
  "_exports": [
    "denoiseq",
    "getSamplesOf",
    "results",
    "setInitValues",
    "setReplicates",
    "setStepSizes",
    "tunedStepSize"
  ],
  "_datasets": [
    {
      "name": "ERCC",
      "title": "ERCC dataset",
      "object": "ERCC",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "A_1",
        "A_2",
        "A_3",
        "A_4",
        "A_5",
        "B_1",
        "B_2",
        "B_3",
        "B_4",
        "B_5"
      ],
      "rows": 92,
      "table": true,
      "tojson": true
    },
    {
      "name": "simdat",
      "title": "simulated data",
      "object": "simdat",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "A1",
        "A2",
        "A3",
        "A4",
        "A5",
        "B1",
        "B2",
        "B3",
        "B4",
        "B5"
      ],
      "rows": 750,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "denoiseq",
      "title": "Differential expression analysis using a bottom-up model",
      "topics": [
        "denoiseq"
      ]
    },
    {
      "page": "ERCC",
      "title": "ERCC dataset",
      "topics": [
        "ERCC"
      ]
    },
    {
      "page": "getSamplesOf",
      "title": "Get posterior samples of a parameter",
      "topics": [
        "getSamplesOf"
      ]
    },
    {
      "page": "readsData",
      "title": "An S4 class to represent summarised counts and the output of Bayesian inference.",
      "topics": [
        "readsData"
      ]
    },
    {
      "page": "results",
      "title": "Compute the test statistic",
      "topics": [
        "results"
      ]
    },
    {
      "page": "setInitValues",
      "title": "Generic for altering the initValues slot",
      "topics": [
        "setInitValues",
        "setInitValues,readsData-method"
      ]
    },
    {
      "page": "setOutput-readsData-method",
      "title": "Mutator method for the output slot of the readsData object.",
      "topics": [
        "setOutput,readsData-method"
      ]
    },
    {
      "page": "setReplicates",
      "title": "Generic for the altering setReplicates slot.",
      "topics": [
        "setReplicates",
        "setReplicates,readsData-method"
      ]
    },
    {
      "page": "setReplicates-readsData-method",
      "title": "Mutator method for the replicates slot of the readsData object.",
      "topics": [
        "setReplicates,readsData-method"
      ]
    },
    {
      "page": "setStepSizes",
      "title": "Generic for altering the stepSizes slot.",
      "topics": [
        "setStepSizes",
        "setStepSizes,readsData-method"
      ]
    },
    {
      "page": "setStepSizes-readsData-method",
      "title": "Mutator method for the stepSizes slot of the readsData object.",
      "topics": [
        "setStepSizes,readsData-method"
      ]
    },
    {
      "page": "simdat",
      "title": "simulated data",
      "topics": [
        "simdat"
      ]
    },
    {
      "page": "tunedStepSize",
      "title": "Get values of the tuned step sizes.",
      "topics": [
        "tunedStepSize"
      ]
    }
  ],
  "_readme": "https://github.com/buriom/denoiseq/raw/HEAD/README.md",
  "_rundeps": [],
  "_vignettes": [
    {
      "source": "denoiSeq-vignette.Rmd",
      "filename": "denoiSeq-vignette.html",
      "title": "denoiSeq: Differential expression analysis using a bottom-up approach",
      "author": "Gershom Buri, Wilfred Ndifon",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Diagnostics"
      ],
      "created": "2017-05-03 13:57:14",
      "modified": "2018-01-17 14:41:06",
      "commits": 12
    }
  ],
  "_score": 3.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "denoiseq",
  "_universes": [
    "buriom"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-06-04T10:51:15.000Z",
      "distro": "noble",
      "commit": "96e629965741d4cf90bfe03722d3d004d4990a9b",
      "fileid": "f0c71fc8a60b24d4d809464b03768f3405f71425a5788fde977aa13f9b7aa3ce",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/buriom/actions/runs/26946974774"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-06-04T10:51:06.000Z",
      "distro": "noble",
      "commit": "96e629965741d4cf90bfe03722d3d004d4990a9b",
      "fileid": "7451fdc263aa1b98f24839e21eca2e865f74a091aac60e84b70069f9f46e262e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/buriom/actions/runs/26946974774"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-06-04T10:51:10.000Z",
      "commit": "96e629965741d4cf90bfe03722d3d004d4990a9b",
      "fileid": "797eeacbd4805387fefb7828617e1c3d7b199c8e12fd537ca6d195739c8c9a4f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/buriom/actions/runs/26946974774"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-06-04T10:51:14.000Z",
      "commit": "96e629965741d4cf90bfe03722d3d004d4990a9b",
      "fileid": "9d046f47ae697e7983e9427fa736a521ddee6f1b4001139d7256e056ca752ed2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/buriom/actions/runs/26946974774"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.1",
      "date": "2026-06-04T10:50:59.000Z",
      "commit": "96e629965741d4cf90bfe03722d3d004d4990a9b",
      "fileid": "17bd73dd00d99d1c3e57dc3fe289bc7e6598717803064db5b603b442764621e8",
      "status": "success",
      "buildurl": "https://github.com/r-universe/buriom/actions/runs/26946974774"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-06-04T10:52:25.000Z",
      "commit": "96e629965741d4cf90bfe03722d3d004d4990a9b",
      "fileid": "9ade9716fa9a6a5108e7944b8e9414c9e42e62302e1127ee0ff7af3f16b5d0dd",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/buriom/actions/runs/26946974774"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-06-04T10:50:11.000Z",
      "commit": "96e629965741d4cf90bfe03722d3d004d4990a9b",
      "fileid": "d84881ec9b03021fdf4976977198e7819a5fa96d259a56788684c7039419c819",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/buriom/actions/runs/26946974774"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-06-04T10:50:35.000Z",
      "commit": "96e629965741d4cf90bfe03722d3d004d4990a9b",
      "fileid": "edf48879643e67ab1c19d2acee8fc37fade3aad0c632f6bf2c7bc77b62a2c466",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/buriom/actions/runs/26946974774"
    }
  ]
}