{
  "_id": "6a1f310bb401979e73427a82",
  "Package": "switchde",
  "Type": "Package",
  "Title": "Switch-like differential expression across single-cell\ntrajectories",
  "Version": "1.39.0",
  "Date": "2017-10-24",
  "Authors@R": "person(\"Kieran\", \"Campbell\", email =\n\"kieranrcampbell@gmail.com\", role = c(\"aut\", \"cre\"))",
  "Description": "Inference and detection of switch-like differential\nexpression across single-cell RNA-seq trajectories.",
  "License": "GPL (>= 2)",
  "LazyData": "TRUE",
  "biocViews": "ImmunoOncology, Software, Transcriptomics, GeneExpression,\nRNASeq, Regression, DifferentialExpression, SingleCell",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "6.0.1",
  "URL": "https://github.com/kieranrcampbell/switchde",
  "BugReports": "https://github.com/kieranrcampbell/switchde",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:44:01 UTC",
  "RemoteUrl": "https://github.com/bioc/switchde",
  "RemoteRef": "HEAD",
  "RemoteSha": "8527700c44bf8de47ae3410ff51e71a2b1fbfa32",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-15 10:08:31 UTC",
    "User": "root"
  },
  "Author": "Kieran Campbell [aut, cre]",
  "Maintainer": "Kieran Campbell <kieranrcampbell@gmail.com>",
  "MD5sum": "389fc7d4b3e70c58da8dfa17974fd10e",
  "_user": "bioc",
  "_type": "src",
  "_file": "switchde_1.39.0.tar.gz",
  "_fileid": "1edb059dd3ffc46c4cf88132eb64aee8e6645f5c14aad03558228e927e73d9d0",
  "_filesize": 916469,
  "_sha256": "1edb059dd3ffc46c4cf88132eb64aee8e6645f5c14aad03558228e927e73d9d0",
  "_created": "2026-05-15T10:08:31.000Z",
  "_published": "2026-06-02T19:37:47.181Z",
  "_jobs": [
    {
      "job": 79152216266,
      "time": 175,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7014802556"
    },
    {
      "job": 79152216595,
      "time": 314,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7014841778"
    },
    {
      "job": 79152215734,
      "time": 272,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7014830070"
    },
    {
      "job": 79152216376,
      "time": 206,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7014915545"
    },
    {
      "job": 79152215884,
      "time": 236,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7014905485"
    },
    {
      "job": 79152214964,
      "time": 253,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7014754059"
    },
    {
      "job": 79152214933,
      "time": 1435,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 79152216180,
      "time": 208,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7014811778"
    },
    {
      "job": 79152216570,
      "time": 191,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7014806929"
    },
    {
      "job": 79152216210,
      "time": 202,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7014810026"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25912109777",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/switchde",
  "_commit": {
    "id": "8527700c44bf8de47ae3410ff51e71a2b1fbfa32",
    "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": 1777380241
  },
  "_maintainer": {
    "name": "Kieran Campbell",
    "email": "kieranrcampbell@gmail.com",
    "login": "kieranrcampbell",
    "uuid": 2039489
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4",
      "role": "Depends"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Depends"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "numDeriv",
      "role": "Suggests"
    },
    {
      "package": "tidyr",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.39.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.38.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "software",
    "transcriptomics",
    "geneexpression",
    "rnaseq",
    "regression",
    "differentialexpression",
    "singlecell",
    "gene-expression",
    "genomics",
    "single-cell"
  ],
  "_stars": 22,
  "_contributors": [
    {
      "user": "kieranrcampbell",
      "count": 58,
      "uuid": 2039489
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 375,
    "source": "https://www.bioconductor.org/packages/stats/bioc/switchde"
  },
  "_mentions": 5,
  "_devurl": "https://github.com/kieranrcampbell/switchde",
  "_searchresults": 10,
  "_rbuild": "4.6.0",
  "_assets": [
    "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",
    "extra/switchde.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/kieranrcampbell/switchde",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "example_sigmoid",
    "extract_pars",
    "fit_nzi_model",
    "fit_zi_model",
    "switchde",
    "switchplot"
  ],
  "_datasets": [
    {
      "name": "ex_pseudotime",
      "title": "Synthetic gene pseudotimes",
      "object": "ex_pseudotime",
      "class": [
        "array"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "synth_gex",
      "title": "Synthetic gene expression matrix",
      "object": "synth_gex",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "1",
        "2",
        "3",
        "4",
        "5",
        "6",
        "7",
        "8",
        "9",
        "10",
        "11",
        "12",
        "13",
        "14",
        "15",
        "16",
        "17",
        "18",
        "19",
        "20",
        "21",
        "22",
        "23",
        "24",
        "25",
        "26",
        "27",
        "28",
        "29",
        "30",
        "31",
        "32",
        "33",
        "34",
        "35",
        "36",
        "37",
        "38",
        "39",
        "40",
        "41",
        "42",
        "43",
        "44",
        "45",
        "46",
        "47",
        "48",
        "49",
        "50",
        "51",
        "52",
        "53",
        "54",
        "55",
        "56",
        "57",
        "58",
        "59",
        "60",
        "61",
        "62",
        "63",
        "64",
        "65",
        "66",
        "67",
        "68",
        "69",
        "70",
        "71",
        "72",
        "73",
        "74",
        "75",
        "76",
        "77",
        "78",
        "79",
        "80",
        "81",
        "82",
        "83",
        "84",
        "85",
        "86",
        "87",
        "88",
        "89",
        "90",
        "91",
        "92",
        "93",
        "94",
        "95",
        "96",
        "97",
        "98",
        "99",
        "100"
      ],
      "rows": 12,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ex_pseudotime",
      "title": "Synthetic gene pseudotimes",
      "topics": [
        "ex_pseudotime"
      ]
    },
    {
      "page": "example_sigmoid",
      "title": "Example sigmoid plot",
      "topics": [
        "example_sigmoid"
      ]
    },
    {
      "page": "extract_pars",
      "title": "Extract parameters from fitted model",
      "topics": [
        "extract_pars"
      ]
    },
    {
      "page": "fit_nzi_model",
      "title": "Fit a (non-zero-inflated) model for a single gene",
      "topics": [
        "fit_nzi_model"
      ]
    },
    {
      "page": "fit_zi_model",
      "title": "Fit a zero-inflated model for a single gene",
      "topics": [
        "fit_zi_model"
      ]
    },
    {
      "page": "switchde",
      "title": "Switch-like model fitting and differential expression test",
      "topics": [
        "switchde"
      ]
    },
    {
      "page": "switchplot",
      "title": "Plot gene behaviour",
      "topics": [
        "switchplot"
      ]
    },
    {
      "page": "synth_gex",
      "title": "Synthetic gene expression matrix",
      "topics": [
        "synth_gex"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/switchde/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "Biobase",
    "BiocGenerics",
    "cli",
    "cpp11",
    "DelayedArray",
    "dplyr",
    "farver",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "IRanges",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "pillar",
    "pkgconfig",
    "R6",
    "RColorBrewer",
    "rlang",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "SingleCellExperiment",
    "SparseArray",
    "SummarizedExperiment",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "switchde_vignette.Rmd",
      "filename": "switchde_vignette.html",
      "title": "switchde: inference of switch-like gene behaviour along single-cell trajectories",
      "author": "Kieran Campbell",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Pre-filtering of genes",
        "Example usage",
        "Non-zero inflated",
        "Zero-inflation",
        "Controlling the EM algorithm",
        "Use cases",
        "Technical info"
      ],
      "created": "2016-07-15 14:30:19",
      "modified": "2018-08-30 17:57:23",
      "commits": 11
    }
  ],
  "_score": 6.041392685158225,
  "_indexed": true,
  "_nocasepkg": "switchde",
  "_universes": [
    "bioc",
    "kieranrcampbell"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.39.0",
      "date": "2026-05-15T10:11:59.000Z",
      "distro": "noble",
      "commit": "8527700c44bf8de47ae3410ff51e71a2b1fbfa32",
      "fileid": "de3c8c85c3b75e799200ad5cbd610328a1b8e1a03b11318d1eae8a95300af288",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912109777"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.39.0",
      "date": "2026-05-15T10:11:27.000Z",
      "distro": "noble",
      "commit": "8527700c44bf8de47ae3410ff51e71a2b1fbfa32",
      "fileid": "f97ca175081f71171ce6d9523e06ac31160d4e361b6957a0b446d869ae01ed0c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912109777"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.39.0",
      "date": "2026-05-15T10:16:54.000Z",
      "commit": "8527700c44bf8de47ae3410ff51e71a2b1fbfa32",
      "fileid": "3bf32f584a2d86d77c850aa80084a3a6d5303a3719dcd2117069b21669f4aff5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912109777"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.39.0",
      "date": "2026-05-15T10:15:43.000Z",
      "commit": "8527700c44bf8de47ae3410ff51e71a2b1fbfa32",
      "fileid": "58a474f022c9d04a28eabd0d77dc967b34c6fe8af04bad7f24c3464b54e45b8b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912109777"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.39.0",
      "date": "2026-05-15T10:10:18.000Z",
      "commit": "8527700c44bf8de47ae3410ff51e71a2b1fbfa32",
      "fileid": "40cb1203fa8ce34ef6bce720b80caaed1c3e397dff38c8f902e11a43023b0097",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912109777"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.39.0",
      "date": "2026-05-15T10:10:05.000Z",
      "commit": "8527700c44bf8de47ae3410ff51e71a2b1fbfa32",
      "fileid": "6488c041f2be21da55f9c9fa9415531540049b632277011ddc7ce2c1d1751b2b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912109777"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.39.0",
      "date": "2026-05-15T10:10:02.000Z",
      "commit": "8527700c44bf8de47ae3410ff51e71a2b1fbfa32",
      "fileid": "b68e60a7632f7638787e28688ec54ef4578ca82c4c998629f5d2184973dcba67",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912109777"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.39.0",
      "date": "2026-05-22T07:04:04.000Z",
      "commit": "8527700c44bf8de47ae3410ff51e71a2b1fbfa32",
      "fileid": "21ff9151013129d1abfe01d6ea7de590b8c0ab8f2e8422021546a6f71b648bf7",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912109777"
    }
  ]
}