{
  "_id": "6ab0d77f3d719c1f840839a2",
  "Package": "RhyME",
  "Title": "Beta Regression Cosinor Models for Circadian Methylation\nAnalysis",
  "Version": "0.99.0",
  "Authors@R": "person(\"Yixiang\", \"Hong\",\nemail = \"yixiang.hong@uth.tmc.edu\", role = c(\"aut\", \"cre\"))",
  "Description": "Fits cosinor-based beta regression models for detecting\ncircadian rhythmicity in DNA methylation array data using\nTemplate Model Builder (TMB) for efficient likelihood\noptimization. Supports fixed-effects (cross-sectional) and\nmixed-effects (repeated measures) designs with configurable\nperiod and adjustment covariates. Implements empirical Bayes\nshrinkage of the beta distribution precision parameter across\nCpG sites, analogous to limma's moderated variance, to improve\ngenome-wide inference. Provides amplitude, phase, and MESOR\nestimation on both logit-link and response scales.",
  "License": "GPL (>= 3) + file LICENSE",
  "URL": "https://github.com/njuelsdke/RhyME",
  "BugReports": "https://github.com/njuelsdke/RhyME/issues",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "biocViews": "Epigenetics, DNAMethylation, TimeCourse, Regression,\nDifferentialMethylation, Software",
  "VignetteBuilder": "knitr",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://biocstaging.r-universe.dev",
  "Date/Publication": "2026-08-21 22:32:49 UTC",
  "RemoteUrl": "https://github.com/BiocStaging/RhyME",
  "RemoteRef": "HEAD",
  "RemoteSha": "cbe5289e2a0654fc81e8caebc24950e14c84b351",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-09-21 06:53:29 UTC",
    "User": "root"
  },
  "Author": "Yixiang Hong [aut, cre]",
  "Maintainer": "Yixiang Hong <yixiang.hong@uth.tmc.edu>",
  "_user": "biocstaging",
  "_type": "src",
  "_file": "RhyME_0.99.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/72afc3ce513fd56c666797f4dba04f6c053a2ae027304c3e675ca1a22419f8bc",
  "_filesize": 2766856,
  "_sha256": "72afc3ce513fd56c666797f4dba04f6c053a2ae027304c3e675ca1a22419f8bc",
  "_expires": "2026-12-30T07:06:37.000Z",
  "_created": "2026-09-21T06:53:29.000Z",
  "_published": "2026-09-21T07:06:39.148Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 7
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35570089110",
  "_status": "success",
  "_upstream": "https://github.com/BiocStaging/RhyME",
  "_commit": {
    "id": "cbe5289e2a0654fc81e8caebc24950e14c84b351",
    "author": "Yixiang Hong <yxh@yxh.local>",
    "committer": "Yixiang Hong <yxh@yxh.local>",
    "message": "Keep runnable notebooks local\n",
    "time": 1787351569
  },
  "_maintainer": {
    "name": "Yixiang Hong",
    "email": "yixiang.hong@uth.tmc.edu"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 106241022455,
      "time": 280,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10625009486"
    },
    {
      "job": 106241022568,
      "time": 315,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10625961809"
    },
    {
      "job": 106241022560,
      "time": 383,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10625737641"
    },
    {
      "job": 106241022623,
      "time": 320,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10625558825"
    },
    {
      "job": 106241022619,
      "time": 365,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10626365706"
    },
    {
      "job": 106241022675,
      "time": 255,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10625961688"
    },
    {
      "job": 106241022540,
      "time": 565,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10625957568"
    },
    {
      "job": 106241022530,
      "time": 224,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10625588531"
    },
    {
      "job": 106241022582,
      "time": 665,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10626231986"
    },
    {
      "job": 106239766228,
      "time": 355,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10625846442"
    },
    {
      "job": 106241022436,
      "time": 181,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10624779522"
    },
    {
      "job": 106241022741,
      "time": 422,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10626027142"
    },
    {
      "job": 106241022580,
      "time": 365,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10625927057"
    },
    {
      "job": 106241022556,
      "time": 290,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10626206319"
    },
    {
      "job": 106241022575,
      "time": 387,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10625957129"
    },
    {
      "job": 106241022557,
      "time": 349,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10625114579"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3.0",
      "role": "Depends"
    },
    {
      "package": "TMB",
      "role": "LinkingTo"
    },
    {
      "package": "RcppEigen",
      "role": "LinkingTo"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "TMB",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "limma",
      "role": "Suggests"
    },
    {
      "package": "cowplot",
      "role": "Suggests"
    }
  ],
  "_owner": "biocstaging",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-27",
      "n": 17
    },
    {
      "week": "2026-34",
      "n": 15
    }
  ],
  "_tags": [],
  "_topics": [
    "epigenetics",
    "dnamethylation",
    "timecourse",
    "regression",
    "differentialmethylation",
    "software",
    "cpp",
    "openmp"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "njuelsdke",
      "count": 23,
      "uuid": 161998723
    }
  ],
  "_userbio": {
    "uuid": 278472782,
    "type": "organization",
    "name": "BiocStaging",
    "followers": 2
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RhyME"
  },
  "_devurl": "https://github.com/njuelsdke/rhyme",
  "_searchresults": 0,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md",
    "extra/RhyME.html",
    "LICENSE"
  ],
  "_cranurl": false,
  "_exports": [
    "fitCosinor",
    "plotCosinorFit",
    "topCpGs"
  ],
  "_help": [
    {
      "page": "fitCosinor",
      "title": "Fit RhyME across CpG sites",
      "topics": [
        "fitCosinor"
      ]
    },
    {
      "page": "plotCosinorFit",
      "title": "Plot fitted cosinor curves for selected CpGs",
      "topics": [
        "plotCosinorFit"
      ]
    },
    {
      "page": "topCpGs",
      "title": "Return top CpGs by significance",
      "topics": [
        "topCpGs"
      ]
    }
  ],
  "_pkglogo": "https://github.com/BiocStaging/RhyME/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/BiocStaging/RhyME/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "cli",
    "codetools",
    "cpp11",
    "DelayedArray",
    "farver",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "IRanges",
    "isoband",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "rlang",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "TMB",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    },
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_vignettes": [
    {
      "source": "RhyME_vignette.Rmd",
      "filename": "RhyME_vignette.html",
      "title": "Detecting Circadian Rhythmicity in DNA Methylation with RhyME",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Data Preparation",
        "Statistical Model",
        "Empirical-Bayes Precision Shrinkage",
        "Fixed-Effects Analysis",
        "Longitudinal Analysis (Mixed-Effects)",
        "Parameter Estimates and Result Interpretation",
        "Top-ranked CpG sites",
        "Visualization",
        "Session Info"
      ],
      "created": "2026-08-21 19:08:37",
      "modified": "2026-08-21 21:22:28",
      "commits": 10
    }
  ],
  "_score": 3,
  "_indexed": true,
  "_nocasepkg": "rhyme",
  "_universes": [
    "biocstaging",
    "njuelsdke"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.0",
      "date": "2026-09-21T06:57:33.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "cbe5289e2a0654fc81e8caebc24950e14c84b351",
      "fileid": "https://r2.ropensci.org/cc59c41b3c6543bdde7e43b43694ec74275abfd910da979126327b7aa9207943",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35570089110"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.0",
      "date": "2026-09-21T06:58:08.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "cbe5289e2a0654fc81e8caebc24950e14c84b351",
      "fileid": "https://r2.ropensci.org/766f53f309e0c0a901926f7e5b125ab13d5015fee92103957cb3594fd0b603cf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35570089110"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.99.0",
      "date": "2026-09-21T06:57:32.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "cbe5289e2a0654fc81e8caebc24950e14c84b351",
      "fileid": "https://r2.ropensci.org/2fcc5823f1149f38868c8eafd65febd535b4bdfc188669dbff316f1201fa19a5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35570089110"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.99.0",
      "date": "2026-09-21T06:57:35.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "cbe5289e2a0654fc81e8caebc24950e14c84b351",
      "fileid": "https://r2.ropensci.org/b97744f2c49f9a43a34d19f045d27bdc1cc5519eea70fff95bb289de3af0a31f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35570089110"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.0",
      "date": "2026-09-21T06:56:41.000Z",
      "arch": "aarch64",
      "commit": "cbe5289e2a0654fc81e8caebc24950e14c84b351",
      "fileid": "https://r2.ropensci.org/f52f3d85b77a504cd4930b5d11ba795712482bc3a669be527c6f8be80065f1a4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35570089110"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.0",
      "date": "2026-09-21T06:58:13.000Z",
      "arch": "x86_64",
      "commit": "cbe5289e2a0654fc81e8caebc24950e14c84b351",
      "fileid": "https://r2.ropensci.org/46e659da6118f669349b956a0e8cc72ee16ac889f1057db13768af8feff52c5b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35570089110"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.99.0",
      "date": "2026-09-21T06:56:33.000Z",
      "arch": "aarch64",
      "commit": "cbe5289e2a0654fc81e8caebc24950e14c84b351",
      "fileid": "https://r2.ropensci.org/53a19031f512fc7e9c713757116be8ea4019e4cd71ea8d899c4dad9779281542",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35570089110"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.99.0",
      "date": "2026-09-21T06:58:42.000Z",
      "arch": "x86_64",
      "commit": "cbe5289e2a0654fc81e8caebc24950e14c84b351",
      "fileid": "https://r2.ropensci.org/af09cbf84d1aa1d1920f74e3752936dceba0b5e26b0b3a70d9367ee0ea1d837a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35570089110"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.99.0",
      "date": "2026-09-21T06:57:32.000Z",
      "arch": "emscripten",
      "commit": "cbe5289e2a0654fc81e8caebc24950e14c84b351",
      "fileid": "https://r2.ropensci.org/c6e27f3187cdb15439e6841478a0be61c630929f65a12960af73db15acffbd05",
      "status": "success",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35570089110"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.99.0",
      "date": "2026-09-21T06:59:00.000Z",
      "arch": "aarch64",
      "commit": "cbe5289e2a0654fc81e8caebc24950e14c84b351",
      "fileid": "https://r2.ropensci.org/6e4ca9f41a47744311471474dd8fbd23823238f6c319dd87848b3e2f0fee5caf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35570089110"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.99.0",
      "date": "2026-09-21T06:57:04.000Z",
      "arch": "x86_64",
      "commit": "cbe5289e2a0654fc81e8caebc24950e14c84b351",
      "fileid": "https://r2.ropensci.org/d1ca59776b0af723b1b0c573dfc53cda9a33ed5df48ac3f8c66ff9ec864788d7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35570089110"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.99.0",
      "date": "2026-09-21T06:56:19.000Z",
      "arch": "x86_64",
      "commit": "cbe5289e2a0654fc81e8caebc24950e14c84b351",
      "fileid": "https://r2.ropensci.org/370501bd113a83b14519eb3085593eefc68fff62def54017cf499cc08f2e2c6f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35570089110"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.99.0",
      "date": "2026-09-21T06:58:30.000Z",
      "arch": "aarch64",
      "commit": "cbe5289e2a0654fc81e8caebc24950e14c84b351",
      "fileid": "https://r2.ropensci.org/ddd7217f4fc3a09bd722294c9294cb65fb122a7172eaaf3a854ac4286582dda0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35570089110"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.99.0",
      "date": "2026-09-21T06:56:25.000Z",
      "arch": "x86_64",
      "commit": "cbe5289e2a0654fc81e8caebc24950e14c84b351",
      "fileid": "https://r2.ropensci.org/1379b11a55af778070894e7ee9e280a048e0f4581d2f3a32054d195aa4c6ce37",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35570089110"
    }
  ]
}