{
  "_id": "6ad31c432c5c76d3dd0c985f",
  "Package": "limorhyde",
  "Title": "Differential Analysis of Rhythmic Transcriptome Data",
  "Version": "1.0.3",
  "Authors@R": "c(\nperson('Jake', 'Hughey', , 'jakejhughey@gmail.com', c('aut', 'cre')),\nperson('Jordan', 'Singer', , 'jordan.m.singer@vumc.org', 'ctb'))",
  "Description": "A flexible approach, inspired by cosinor regression, for\ndifferential analysis of rhythmic transcriptome data. See\nSinger and Hughey (2018) <doi:10.1177/0748730418813785>.",
  "License": "GPL-2",
  "URL": "https://limorhyde.hugheylab.org,\nhttps://github.com/hugheylab/limorhyde",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "BugReports": "https://github.com/hugheylab/limorhyde/issues",
  "Repository": "https://hugheylab.r-universe.dev",
  "Date/Publication": "2026-01-20 10:07:01 UTC",
  "RemoteUrl": "https://github.com/hugheylab/limorhyde",
  "RemoteRef": "HEAD",
  "RemoteSha": "de51f1b89ac3ebc60a61219cd9e6d8c258f07d4b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-17 06:52:00 UTC",
    "User": "root"
  },
  "Author": "Jake Hughey [aut, cre],\nJordan Singer [ctb]",
  "Maintainer": "Jake Hughey <jakejhughey@gmail.com>",
  "_user": "hugheylab",
  "_type": "src",
  "_file": "limorhyde_1.0.3.tar.gz",
  "_fileid": "https://r2.ropensci.org/6addeda648dda2e49a5b1ef95c9f034c36a0e8c67ea7ae7f29e90538bc6ec4ef",
  "_filesize": 3318611,
  "_sha256": "6addeda648dda2e49a5b1ef95c9f034c36a0e8c67ea7ae7f29e90538bc6ec4ef",
  "_expires": "2027-01-25T06:57:05.000Z",
  "_created": "2026-10-17T06:52:00.000Z",
  "_published": "2026-10-17T06:57:07.199Z",
  "_buildurl": "https://github.com/r-universe/hugheylab/actions/runs/39011252650",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 117334825259,
      "time": 136,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12092563363"
    },
    {
      "job": 117334825322,
      "time": 123,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12093550406"
    },
    {
      "job": 117334825308,
      "time": 118,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12092294719"
    },
    {
      "job": 117334825260,
      "time": 84,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12093415314"
    },
    {
      "job": 117334146538,
      "time": 221,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12092074823"
    },
    {
      "job": 117334825265,
      "time": 113,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12093172335"
    },
    {
      "job": 117334825389,
      "time": 99,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12093470600"
    },
    {
      "job": 117334825333,
      "time": 72,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12093365785"
    },
    {
      "job": 117334825334,
      "time": 89,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12092898402"
    }
  ],
  "_upstream": "https://github.com/hugheylab/limorhyde",
  "_commit": {
    "id": "de51f1b89ac3ebc60a61219cd9e6d8c258f07d4b",
    "author": "Jake Hughey <jakejhughey@gmail.com>",
    "committer": "Jake Hughey <jakejhughey@gmail.com>",
    "message": "remove qs dependency.\n",
    "time": 1768903621
  },
  "_maintainer": {
    "name": "Jake Hughey",
    "email": "jakejhughey@gmail.com",
    "login": "jakejh",
    "description": "",
    "uuid": 2295314
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "pbs",
      "version": ">= 1.1",
      "role": "Imports"
    },
    {
      "package": "annotate",
      "version": ">= 1.58.0",
      "role": "Suggests"
    },
    {
      "package": "data.table",
      "version": ">= 1.12.2",
      "role": "Suggests"
    },
    {
      "package": "foreach",
      "version": ">= 1.4.4",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "version": ">= 2.2.1",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "version": ">= 1.20",
      "role": "Suggests"
    },
    {
      "package": "limma",
      "version": ">= 3.36.1",
      "role": "Suggests"
    },
    {
      "package": "matrixStats",
      "version": ">= 0.56.0",
      "role": "Suggests"
    },
    {
      "package": "org.Mm.eg.db",
      "version": ">= 3.6.0",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "version": ">= 1.9",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.4",
      "role": "Suggests"
    }
  ],
  "_owner": "hugheylab",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-04",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 2,
  "_contributors": [
    {
      "user": "jakejh",
      "count": 55,
      "uuid": 2295314
    },
    {
      "user": "jschoenbachler",
      "count": 45,
      "uuid": 15148457
    }
  ],
  "_userbio": {
    "uuid": 32131222,
    "type": "organization",
    "name": "Hughey Lab",
    "followers": 4
  },
  "_downloads": {
    "count": 335,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/limorhyde"
  },
  "_devurl": "https://github.com/hugheylab/limorhyde",
  "_searchresults": 22,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/limorhyde.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/hugheylab/limorhyde",
  "_realowner": "hugheylab",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.1",
      "date": "2022-02-18"
    },
    {
      "version": "1.0.3",
      "date": "2026-01-20"
    }
  ],
  "_exports": [
    "getCosinorBasis",
    "getSplineBasis",
    "limorhyde"
  ],
  "_help": [
    {
      "page": "getCosinorBasis",
      "title": "Basis matrix for cosinor",
      "topics": [
        "getCosinorBasis"
      ]
    },
    {
      "page": "getSplineBasis",
      "title": "Basis matrix for periodic splines",
      "topics": [
        "getSplineBasis"
      ]
    },
    {
      "page": "limorhyde",
      "title": "Convert a periodic time variable into components usable in linear models",
      "topics": [
        "limorhyde"
      ]
    }
  ],
  "_readme": "https://github.com/hugheylab/limorhyde/raw/HEAD/README.md",
  "_rundeps": [
    "pbs"
  ],
  "_vignettes": [
    {
      "source": "introduction.Rmd",
      "filename": "introduction.html",
      "title": "Analyzing circadian transcriptome data with LimoRhyde",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Load packages and set parameters",
        "Load the data",
        "Identify rhythmic genes",
        "Identify differentially rhythmic genes",
        "Identify differentially expressed genes",
        "Plot the results"
      ],
      "created": "2018-08-29 16:27:03",
      "modified": "2026-01-20 10:07:01",
      "commits": 8
    }
  ],
  "_score": 4.342422680822207,
  "_indexed": true,
  "_nocasepkg": "limorhyde",
  "_universes": [
    "hugheylab",
    "jakejh"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.3",
      "date": "2026-10-17T06:54:22.000Z",
      "distro": "resolute",
      "commit": "de51f1b89ac3ebc60a61219cd9e6d8c258f07d4b",
      "fileid": "https://r2.ropensci.org/94699efad17fdcf538883694e60063406658a758b91b1c0a2b14db39f1f4d329",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/39011252650"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.3",
      "date": "2026-10-17T06:54:10.000Z",
      "distro": "resolute",
      "commit": "de51f1b89ac3ebc60a61219cd9e6d8c258f07d4b",
      "fileid": "https://r2.ropensci.org/cd06d0b1819f90e0b4fe88b74c5f63082ab7bba6bfad0f7da5240e4cbac7210d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/39011252650"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.3",
      "date": "2026-10-17T06:56:34.000Z",
      "commit": "de51f1b89ac3ebc60a61219cd9e6d8c258f07d4b",
      "fileid": "https://r2.ropensci.org/86c75134277705e87f1bcb9b22a822c11cd5eb306f1478961bcb9e66098ba3be",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/39011252650"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0.3",
      "date": "2026-10-17T06:54:51.000Z",
      "commit": "de51f1b89ac3ebc60a61219cd9e6d8c258f07d4b",
      "fileid": "https://r2.ropensci.org/5f3c3e1972b3510a1249f65624ad0bdb7cd5cb19dea514a62a385e952eb4c185",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/39011252650"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.3",
      "date": "2026-10-17T06:54:08.000Z",
      "commit": "de51f1b89ac3ebc60a61219cd9e6d8c258f07d4b",
      "fileid": "https://r2.ropensci.org/b45702527b7a04646d3f286efbfe4037a761494d2818c1c5f0462c040141ce45",
      "status": "success",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/39011252650"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-10-17T06:53:40.000Z",
      "commit": "de51f1b89ac3ebc60a61219cd9e6d8c258f07d4b",
      "fileid": "https://r2.ropensci.org/26efe234b5f316b6e5dde9e075e9088c8137a9fb2191a974fc361e37c62304b3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/39011252650"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-10-17T06:53:18.000Z",
      "commit": "de51f1b89ac3ebc60a61219cd9e6d8c258f07d4b",
      "fileid": "https://r2.ropensci.org/7d6c0d3f3b6f6bf211e16c2f387038ec9e17e8206bb6353ccc8c4177b433ca27",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/39011252650"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-10-17T06:53:31.000Z",
      "commit": "de51f1b89ac3ebc60a61219cd9e6d8c258f07d4b",
      "fileid": "https://r2.ropensci.org/cc5cc4d23124f3c8819abd6ebe51095674f757c87d4d941cf67ad8d9849dbc59",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/hugheylab/actions/runs/39011252650"
    }
  ]
}