{
  "_id": "6a17de91acfb0bcc41d9cfd5",
  "Package": "DEsingle",
  "Type": "Package",
  "Title": "DEsingle for detecting three types of differential expression in\nsingle-cell RNA-seq data",
  "Version": "1.33.0",
  "Date": "2018-12-01",
  "Author": "Zhun Miao <miaoz13@tsinghua.org.cn>",
  "Maintainer": "Zhun Miao <miaoz13@tsinghua.org.cn>",
  "Description": "DEsingle is an R package for differential expression (DE)\nanalysis of single-cell RNA-seq (scRNA-seq) data. It defines\nand detects 3 types of differentially expressed genes between\ntwo groups of single cells, with regard to different expression\nstatus (DEs), differential expression abundance (DEa), and\ngeneral differential expression (DEg). DEsingle employs\nZero-Inflated Negative Binomial model to estimate the\nproportion of real and dropout zeros and to define and detect\nthe 3 types of DE genes. Results showed that DEsingle\noutperforms existing methods for scRNA-seq DE analysis, and can\nreveal different types of DE genes that are enriched in\ndifferent biological functions.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "URL": "https://miaozhun.github.io/DEsingle/",
  "biocViews": "DifferentialExpression, GeneExpression, SingleCell,\nImmunoOncology, RNASeq, Transcriptomics, Sequencing,\nPreprocessing, Software",
  "RoxygenNote": "6.0.1",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:47:40 UTC",
  "RemoteUrl": "https://github.com/bioc/DEsingle",
  "RemoteRef": "HEAD",
  "RemoteSha": "f478013f7131d27856ee3b1cab0048fae87a37f5",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-28 06:13:07 UTC",
    "User": "root"
  },
  "MD5sum": "d69fcd33ca40149cecdc17506a6d273d",
  "_user": "bioc",
  "_type": "src",
  "_file": "DEsingle_1.33.0.tar.gz",
  "_fileid": "a1d10b7d0f514819f3d9ee9ff9c06205499749bc6804bbc673a4f31b131a644d",
  "_filesize": 199330,
  "_sha256": "a1d10b7d0f514819f3d9ee9ff9c06205499749bc6804bbc673a4f31b131a644d",
  "_created": "2026-05-28T06:13:07.000Z",
  "_published": "2026-05-28T06:20:01.702Z",
  "_jobs": [
    {
      "job": 78234343406,
      "time": 147,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7258956264"
    },
    {
      "job": 78234343480,
      "time": 268,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7258984704"
    },
    {
      "job": 78234343521,
      "time": 291,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7258990169"
    },
    {
      "job": 78234343461,
      "time": 189,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7259009995"
    },
    {
      "job": 78234343421,
      "time": 192,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7259010804"
    },
    {
      "job": 78233909516,
      "time": 223,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7258922613"
    },
    {
      "job": 78234343415,
      "time": 129,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7258951993"
    },
    {
      "job": 78234343515,
      "time": 240,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7258978087"
    },
    {
      "job": 78234343446,
      "time": 224,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7258974079"
    },
    {
      "job": 78234343441,
      "time": 273,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7258985999"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 3,
    "note": 10
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26557970100",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/DEsingle",
  "_commit": {
    "id": "f478013f7131d27856ee3b1cab0048fae87a37f5",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380460
  },
  "_maintainer": {
    "name": "Zhun Miao",
    "email": "miaoz13@tsinghua.org.cn"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4.0",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "version": ">= 1.2-14",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "version": ">= 7.3-45",
      "role": "Imports"
    },
    {
      "package": "VGAM",
      "version": ">= 1.0-2",
      "role": "Imports"
    },
    {
      "package": "bbmle",
      "version": ">= 1.0.18",
      "role": "Imports"
    },
    {
      "package": "gamlss",
      "version": ">= 4.4-0",
      "role": "Imports"
    },
    {
      "package": "maxLik",
      "version": ">= 1.3-4",
      "role": "Imports"
    },
    {
      "package": "pscl",
      "version": ">= 1.4.9",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "version": ">= 1.12.0",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.33.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.32.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "differentialexpression",
    "geneexpression",
    "singlecell",
    "immunooncology",
    "rnaseq",
    "transcriptomics",
    "sequencing",
    "preprocessing",
    "software"
  ],
  "_stars": 33,
  "_contributors": [
    {
      "user": "miaozhun",
      "count": 221,
      "uuid": 28986481
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 2,
      "uuid": 1744257
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 611,
    "source": "https://www.bioconductor.org/packages/stats/bioc/DEsingle"
  },
  "_mentions": 15,
  "_devurl": "https://github.com/miaozhun/desingle",
  "_searchresults": 38,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/DEsingle.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/miaozhun/desingle",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "DEsingle",
    "DEtype"
  ],
  "_datasets": [
    {
      "name": "counts",
      "title": "TestData: A test dataset for DEsingle",
      "object": "TestData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "E3.46.3383",
        "E3.51.3425",
        "E3.46.3388",
        "E3.51.3423",
        "E3.46.3382",
        "E3.49.3407",
        "E3.47.3393",
        "E3.46.3384",
        "E3.45.3374",
        "E3.48.3401",
        "E3.53.3436",
        "E3.50.3413",
        "E3.45.3379",
        "E3.4.462",
        "E3.52.3429",
        "E3.52.3428",
        "E3.45.3378",
        "E3.1.448",
        "E3.51.3421",
        "E3.45.3380",
        "E3.2.453",
        "E3.47.3394",
        "E3.49.3405",
        "E3.52.3433",
        "E3.50.3416",
        "E3.48.3398",
        "E3.3.456",
        "E3.45.3376",
        "E3.48.3397",
        "E3.2.454",
        "E3.47.3389",
        "E3.49.3403",
        "E3.3.457",
        "E3.2.452",
        "E3.2.455",
        "E3.2.466",
        "E3.49.3409",
        "E3.47.3395",
        "E3.2.467",
        "E3.52.3434",
        "E3.52.3431",
        "E3.53.3435",
        "E3.52.3430",
        "E3.48.3399",
        "E3.51.3422",
        "E3.53.3438",
        "E3.47.3391",
        "E3.2.449",
        "E3.49.3408",
        "E3.50.3415",
        "E4.late.33.3164",
        "E4.late.34.3186",
        "E4.31_5_1.3",
        "E4.8.1175",
        "E4.24_5_0_4.2",
        "E4.5.522",
        "E4.late.34.3182",
        "E4.9.1212",
        "E4.4.502",
        "E4.late.34.3188",
        "E4.late.33.3163",
        "E4.4.497",
        "E4.1.1",
        "E4.7.643",
        "E4.4.507",
        "E4.late.34.3178",
        "E4.3.485",
        "E4.4.500",
        "E4.9.1211",
        "E4.late.34.3181",
        "E4.8.1179",
        "E4.late.35.3202",
        "E4.late.34.3179",
        "E4.11.1258",
        "E4.late.35.3208",
        "E4.6.616",
        "E4.late.35.3197",
        "E4.late.35.3200",
        "E4.late.34.3176",
        "E4.10.1232",
        "E4.3.488",
        "E4.9.1209",
        "E4.4.509",
        "E4.late.35.3199",
        "E4.24_5_0_4.1",
        "E4.9.1197",
        "E4.3.487",
        "E4.5.524",
        "E4.10.1229",
        "E4.late.35.3196",
        "E4.24_5_0_4.7",
        "E4.late.34.3185",
        "E4.late.33.3161",
        "E4.4.495",
        "E4.31_5_1.2",
        "E4.late.34.3184",
        "E4.3.480",
        "E4.8.1190",
        "E4.late.34.3174",
        "E4.7.648",
        "E4.8.1181",
        "E4.late.35.3201",
        "E4.8.1177",
        "E4.late.35.3212",
        "E4.late.34.3180",
        "E4.1.7",
        "E4.6.613",
        "E4.2.10",
        "E4.6.609",
        "E4.5.512",
        "E4.3.476",
        "E4.3.472",
        "E4.31_5_1.9",
        "E4.8.1192",
        "E4.late.34.3183",
        "E4.5.520",
        "E4.6.627",
        "E4.5.510",
        "E4.late.33.3166",
        "E4.8.1193",
        "E4.4.498",
        "E4.late.33.3159",
        "E4.8.1180",
        "E4.4.501",
        "E4.1.4",
        "E4.5.525",
        "E4.4.503",
        "E4.late.33.3157",
        "E4.8.1183",
        "E4.9.1204",
        "E4.10.1221",
        "E4.5.521",
        "E4.8.1182",
        "E4.31_5_1.8",
        "E4.10.1230",
        "E4.24_5_0_4.3",
        "E4.7.647",
        "E4.3.481",
        "E4.5.518",
        "E4.late.34.3190",
        "E4.8.1189",
        "E4.late.33.3162",
        "E4.24_5_0_4.12",
        "E4.9.1207",
        "E4.8.1173",
        "E4.3.473",
        "E4.8.1194",
        "E4.10.1227",
        "E4.7.646",
        "E4.9.1208"
      ],
      "rows": 200,
      "table": true,
      "tojson": true
    },
    {
      "name": "group",
      "title": "TestData: A test dataset for DEsingle",
      "object": "TestData",
      "class": [
        "factor"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "DEsingle",
      "title": "DEsingle: Detecting differentially expressed genes from scRNA-seq data",
      "topics": [
        "DEsingle"
      ]
    },
    {
      "page": "DEtype",
      "title": "DEtype: Classifying differentially expressed genes from DEsingle",
      "topics": [
        "DEtype"
      ]
    },
    {
      "page": "TestData",
      "title": "TestData: A test dataset for DEsingle",
      "topics": [
        "counts",
        "group",
        "TestData"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/DEsingle/raw/HEAD/README.md",
  "_rundeps": [
    "bbmle",
    "bdsmatrix",
    "BH",
    "BiocParallel",
    "codetools",
    "cpp11",
    "digest",
    "formatR",
    "futile.logger",
    "futile.options",
    "gamlss",
    "gamlss.data",
    "gamlss.dist",
    "generics",
    "lambda.r",
    "lattice",
    "MASS",
    "Matrix",
    "maxLik",
    "miscTools",
    "mvtnorm",
    "nlme",
    "numDeriv",
    "pscl",
    "sandwich",
    "snow",
    "survival",
    "VGAM",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "DEsingle.Rmd",
      "filename": "DEsingle.html",
      "title": "DEsingle",
      "author": "Zhun Miao",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Citation",
        "Installation",
        "Input",
        "Test data",
        "Usage",
        "With read counts matrix input",
        "With SingleCellExperiment input",
        "Output",
        "Parallelization",
        "For Unix and Mac users",
        "For Windows users",
        "Visualization of results",
        "Interpretation of results",
        "Help",
        "Author",
        "Session info"
      ],
      "created": "2018-02-07 08:12:38",
      "modified": "2020-05-20 11:35:10",
      "commits": 22
    }
  ],
  "_score": 7.575418791214361,
  "_indexed": true,
  "_nocasepkg": "desingle",
  "_universes": [
    "bioc",
    "miaozhun"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.33.0",
      "date": "2026-05-28T06:15:59.000Z",
      "distro": "noble",
      "commit": "f478013f7131d27856ee3b1cab0048fae87a37f5",
      "fileid": "46548453ec16ea6c0b1bc78a61ae6a4706936e700faa2c46a5cc0de6aeeada5a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557970100"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.33.0",
      "date": "2026-05-28T06:16:30.000Z",
      "distro": "noble",
      "commit": "f478013f7131d27856ee3b1cab0048fae87a37f5",
      "fileid": "19072df7f0e2c0aa4c01d8fae8c6700cae463562dc6328590f40742b65c49f62",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557970100"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.33.0",
      "date": "2026-05-28T06:18:16.000Z",
      "commit": "f478013f7131d27856ee3b1cab0048fae87a37f5",
      "fileid": "0112e435a304491c1acf3bcfa654ba2ce64b24d91649676c6b54225de7e101ef",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557970100"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.33.0",
      "date": "2026-05-28T06:18:18.000Z",
      "commit": "f478013f7131d27856ee3b1cab0048fae87a37f5",
      "fileid": "8b02afa4d9948572b39c7c5656fd349eaf577a8eca1baf243db57b3c3c120d2b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557970100"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.33.0",
      "date": "2026-05-28T06:15:39.000Z",
      "commit": "f478013f7131d27856ee3b1cab0048fae87a37f5",
      "fileid": "b6f233fe2eb04f190044eb84c343b4e6729594f7c391be799f19884222d9b7ba",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557970100"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-05-28T06:14:52.000Z",
      "commit": "f478013f7131d27856ee3b1cab0048fae87a37f5",
      "fileid": "a8977b375e8882aab28ffcd4cad7f2d6124e3e3eee8f7122411a41745a2681d3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557970100"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-05-28T06:14:40.000Z",
      "commit": "f478013f7131d27856ee3b1cab0048fae87a37f5",
      "fileid": "c4b1d3ae07a77fc75cf532bb17eafa602b77c660b4f6bf363db16bda8c36050c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557970100"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-05-28T06:15:20.000Z",
      "commit": "f478013f7131d27856ee3b1cab0048fae87a37f5",
      "fileid": "8f711d448fe93eb33bbc0919e56526cb299e78e6e1821af9f36d80e2db4de5e6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557970100"
    }
  ]
}