{
  "_id": "6ae8db99818c9e3ef6dbe5f1",
  "Package": "seqRdna",
  "Title": "Tools for Calculating for rDNA in Sequencing Data",
  "Version": "0.99.5",
  "Authors@R": "c(\nperson(\ngiven = \"Daniel\",\nfamily = \"Vaughan\",\nrole = c(\"aut\", \"cre\"),\nemail = \"daniel.1.vaughan@kcl.ac.uk\",\ncomment = c(ORCID = \"0009-0001-6165-2024\")\n),\nperson(\ngiven = \"Medical Research Council (MRC)\",\nrole = \"fnd\"\n)\n)",
  "Description": "Functions for working with rDNA data generated from\nsequencing experiments. The package includes functions to\ncalculate the relative rDNA copy number from coverage data, as\nwell as functions to calculate the absolute rDNA copy number\nusing methylation data.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "URL": "https://github.com/MuscleOmicsLab/seqRdna",
  "BugReports": "https://github.com/MuscleOmicsLab/seqRdna/issues",
  "Config/roxygen2/version": "8.1.1",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, DNAMethylation, Epigenetics, CopyNumberVariation,\nSequencing, Coverage",
  "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://biocstaging.r-universe.dev",
  "Date/Publication": "2026-11-02 12:25:32 UTC",
  "RemoteUrl": "https://github.com/BiocStaging/seqRdna",
  "RemoteRef": "HEAD",
  "RemoteSha": "056ef164e484158823c2bb3b9d44009fb0dbb388",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-11-02 18:44:47 UTC",
    "User": "root"
  },
  "Author": "Daniel Vaughan [aut, cre] (ORCID:\n<https://orcid.org/0009-0001-6165-2024>),\nMedical Research Council (MRC) [fnd]",
  "Maintainer": "Daniel Vaughan <daniel.1.vaughan@kcl.ac.uk>",
  "_user": "biocstaging",
  "_type": "src",
  "_file": "seqRdna_0.99.5.tar.gz",
  "_fileid": "https://r2.ropensci.org/1b1e676bbcafe5a5d7f69b2df77bfc1d30c5d6304cd905125495dbe33a18b243",
  "_filesize": 2876168,
  "_sha256": "1b1e676bbcafe5a5d7f69b2df77bfc1d30c5d6304cd905125495dbe33a18b243",
  "_expires": "2027-02-10T18:51:03.000Z",
  "_created": "2026-11-02T18:44:47.000Z",
  "_published": "2026-11-02T18:51:05.495Z",
  "_upstream": "https://github.com/BiocStaging/seqRdna",
  "_status": "success",
  "_maintainer": {
    "name": "Daniel Vaughan",
    "email": "daniel.1.vaughan@kcl.ac.uk",
    "login": "danvau98",
    "description": "Postdoctoral researcher in Muscle Omics",
    "uuid": 59915690,
    "orcid": "0009-0001-6165-2024"
  },
  "_jobs": [
    {
      "job": 125476909038,
      "time": 177,
      "config": "bioc-checks",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13170611502"
    },
    {
      "job": 125476909126,
      "time": 246,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "13169847521"
    },
    {
      "job": 125476909193,
      "time": 196,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13169357918"
    },
    {
      "job": 125476909210,
      "time": 129,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "13170756360"
    },
    {
      "job": 125476909088,
      "time": 154,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13169242966"
    },
    {
      "job": 125474647316,
      "time": 255,
      "config": "source",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13170870386"
    },
    {
      "job": 125476909053,
      "time": 158,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13169972619"
    },
    {
      "job": 125476909387,
      "time": 154,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "13169842773"
    },
    {
      "job": 125476909251,
      "time": 180,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "13170117363"
    },
    {
      "job": 125476909160,
      "time": 156,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13169917287"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 3
  },
  "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/41502849834",
  "_commit": {
    "id": "056ef164e484158823c2bb3b9d44009fb0dbb388",
    "author": "danvau98 <daniel.1.vaughan@kcl.ac.uk>",
    "committer": "danvau98 <daniel.1.vaughan@kcl.ac.uk>",
    "message": "Updating title in DESCRIPTION.\n",
    "time": 1793622332
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "methylKit",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "glmmTMB",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "biocstaging",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-29",
      "n": 5
    },
    {
      "week": "2026-33",
      "n": 4
    },
    {
      "week": "2026-34",
      "n": 9
    },
    {
      "week": "2026-39",
      "n": 3
    },
    {
      "week": "2026-40",
      "n": 36
    },
    {
      "week": "2026-43",
      "n": 1
    },
    {
      "week": "2026-44",
      "n": 17
    },
    {
      "week": "2026-45",
      "n": 4
    }
  ],
  "_tags": [],
  "_topics": [
    "software",
    "dnamethylation",
    "epigenetics",
    "copynumbervariation",
    "sequencing",
    "coverage"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "danvau98",
      "count": 103,
      "uuid": 59915690
    }
  ],
  "_userbio": {
    "uuid": 278472782,
    "type": "organization",
    "name": "BiocStaging",
    "followers": 3
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/seqRdna"
  },
  "_devurl": "https://github.com/muscleomicslab/seqrdna",
  "_searchresults": 3,
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/seqRdna.html",
    "LICENSE"
  ],
  "_cranurl": false,
  "_exports": [
    "absolute_rDNA_CN",
    "calculate_aggregate_meth",
    "coverage_chr",
    "diff_meth",
    "distribution_log_odd",
    "get_rDNA_data",
    "get_unique_chr_names",
    "relative_rDNA_CN",
    "shifting",
    "sort_by_rDNA_region"
  ],
  "_help": [
    {
      "page": "absolute_rDNA_CN",
      "title": "Calculate Absolute rDNA Copy Number",
      "topics": [
        "absolute_rDNA_CN"
      ]
    },
    {
      "page": "aggregate_numCs_numTs_region",
      "title": "Aggregate methylated and unmethylated counts within a genomic region",
      "topics": [
        "aggregate_numCs_numTs_region"
      ]
    },
    {
      "page": "analyze_methylation_regions",
      "title": "Analyze Methylation Across Genomic Regions",
      "topics": [
        "analyze_methylation_regions"
      ]
    },
    {
      "page": "calculate_aggregate_meth",
      "title": "Computes the aggregate methylation for a specified genomic region across samples, grouped by their respective conditions.",
      "topics": [
        "calculate_aggregate_meth"
      ]
    },
    {
      "page": "coverage_chr",
      "title": "Plot Average Coverage per Chromosome",
      "topics": [
        "coverage_chr"
      ]
    },
    {
      "page": "diff_meth",
      "title": "Differential Methylation Analysis of Ribosomal DNA",
      "topics": [
        "diff_meth"
      ]
    },
    {
      "page": "diff_meth_region",
      "title": "Perform Differential Methylation Analysis for a Genomic Region",
      "topics": [
        "diff_meth_region"
      ]
    },
    {
      "page": "diff_meth_site",
      "title": "Perform Differential Methylation Analysis at Individual Sites",
      "topics": [
        "diff_meth_site"
      ]
    },
    {
      "page": "distribution_log_odd",
      "title": "Calculate Log-Odds of Methylation for a Chromosome",
      "topics": [
        "distribution_log_odd"
      ]
    },
    {
      "page": "extract_site_data",
      "title": "Extract Methylation Site Data for a Genomic Region",
      "topics": [
        "extract_site_data"
      ]
    },
    {
      "page": "get_rDNA_data",
      "title": "Extract rDNA Chromosome Data",
      "topics": [
        "get_rDNA_data"
      ]
    },
    {
      "page": "get_unique_chr_names",
      "title": "Get Unique Chromosome Names and Check Consistency",
      "topics": [
        "get_unique_chr_names"
      ]
    },
    {
      "page": "relative_rDNA_CN",
      "title": "Calculate Relative rDNA Copy Number",
      "topics": [
        "relative_rDNA_CN"
      ]
    },
    {
      "page": "shifting",
      "title": "Shift rDNA Methylation Data",
      "topics": [
        "shifting"
      ]
    },
    {
      "page": "sort_by_rDNA_region",
      "title": "Sort Methylation Data by rDNA Regions",
      "topics": [
        "sort_by_rDNA_region"
      ]
    }
  ],
  "_readme": "https://github.com/BiocStaging/seqRdna/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "backports",
    "bbmle",
    "bdsmatrix",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "boot",
    "broom",
    "cigarillo",
    "cli",
    "coda",
    "codetools",
    "colorspace",
    "cowplot",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "Deriv",
    "doBy",
    "dplyr",
    "emdbook",
    "farver",
    "fastseg",
    "forecast",
    "formatR",
    "fracdiff",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicRanges",
    "ggplot2",
    "glmmTMB",
    "glue",
    "gtable",
    "gtools",
    "httr",
    "IRanges",
    "isoband",
    "jsonlite",
    "KernSmooth",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "lme4",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "mclust",
    "methylKit",
    "mgcv",
    "mime",
    "minqa",
    "modelr",
    "mvtnorm",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "openssl",
    "pbkrtest",
    "pillar",
    "pkgconfig",
    "plyr",
    "purrr",
    "qvalue",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "RCurl",
    "Rdpack",
    "reformulas",
    "reshape2",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RTMB",
    "rtracklayer",
    "S4Vectors",
    "S7",
    "sandwich",
    "scales",
    "Seqinfo",
    "snow",
    "statmod",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "TMB",
    "urca",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XML",
    "XVector",
    "yaml",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "myoRDNA-introduction.Rmd",
      "filename": "myoRDNA-introduction.html",
      "title": "Introduction to seqRdna",
      "author": "MuscleOmicsLab",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Package functionality",
        "Installation",
        "Overview of the analytical workflow",
        "Loading your data into seqRdna",
        "Step 1: Load the example methylation dataset",
        "Step 2: Define experimental conditions",
        "Step 3: Construct a methylRawList object",
        "Step 4: Extract rDNA methylation data",
        "Difference between autosomes and rDNA",
        "Step 5: Adjust rDNA genomic coordinates",
        "rDNA copy-number analysis",
        "Absolute rDNA copy number",
        "Calculating absolute copy number",
        "Relative rDNA copy number",
        "Calculating relative copy number",
        "Considerations for copy-number estimation",
        "Regional rDNA methylation analysis",
        "Step 1: Partition rDNA into genomic regions",
        "rDNA regions",
        "Step 2: Calculate aggregate methylation metrics",
        "Mathematical formulation of methylation proportions",
        "Mean methylation proportion",
        "Median methylation proportion",
        "Differential rDNA methylation analysis",
        "Statistical methodology",
        "Binomial logistic regression",
        "$$\\operatorname{logit}(p_i)",
        "\\log\\left(\\frac{p_i}{1-p_i}\\right)",
        "$$\\operatorname{Var}(Y_i)",
        "Quasi-binomial logistic regression",
        "$$\\boxed{\\operatorname{Var}(Y_i)",
        "$$\\widehat",
        "Beta-binomial logistic regression",
        "Step 1: Site-level differential methylation",
        "Step 2: Region-level differential methylation",
        "$$M_",
        "$$U_",
        "Step 3: Interpreting differential methylation",
        "$$\\widehat",
        "$$\\widehat",
        "$$\\boxed",
        "100\\left(\\widehat",
        "Step 4: Multiple-testing correction",
        "Beta-binomial optimisation and model diagnostics",
        "Available optimisation algorithms",
        "Assessing model convergence",
        "Session information"
      ],
      "created": "2026-09-29 14:13:02",
      "modified": "2026-11-02 09:29:08",
      "commits": 5
    }
  ],
  "_score": 3.6020599913279625,
  "_indexed": true,
  "_nocasepkg": "seqrdna",
  "_universes": [
    "biocstaging",
    "danvau98",
    "muscleomicslab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.5",
      "date": "2026-11-02T18:48:50.000Z",
      "distro": "resolute",
      "commit": "056ef164e484158823c2bb3b9d44009fb0dbb388",
      "fileid": "https://r2.ropensci.org/d574786b2b4a62e86ed62c728644e634b2c1385484ff4dc9bf1acc75c7d72561",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/41502849834"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "0.99.5",
      "date": "2026-11-02T18:48:44.000Z",
      "distro": "resolute",
      "commit": "056ef164e484158823c2bb3b9d44009fb0dbb388",
      "fileid": "https://r2.ropensci.org/ad1c7fa19d6ea413b8db6da7006fcabb4d3acbaa0f6be6946a093f98dd8debbf",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/41502849834"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.5",
      "date": "2026-11-02T18:50:07.000Z",
      "commit": "056ef164e484158823c2bb3b9d44009fb0dbb388",
      "fileid": "https://r2.ropensci.org/6237369dac5f9f7bbb8ce4b92384ad17558feb85ca18d5934e1fae6290007683",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/41502849834"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "0.99.5",
      "date": "2026-11-02T18:48:15.000Z",
      "commit": "056ef164e484158823c2bb3b9d44009fb0dbb388",
      "fileid": "https://r2.ropensci.org/22702c0c3835c35fa02afd1e5c8e3c5680aeab5bf562e188161c843cf0bd87c1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/41502849834"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.99.5",
      "date": "2026-11-02T18:48:34.000Z",
      "commit": "056ef164e484158823c2bb3b9d44009fb0dbb388",
      "fileid": "https://r2.ropensci.org/218b96bc3daa09e6d1386fe8a3f823fb12dadbcce9a8e861864d914db8aa0369",
      "status": "success",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/41502849834"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.99.5",
      "date": "2026-11-02T18:47:49.000Z",
      "commit": "056ef164e484158823c2bb3b9d44009fb0dbb388",
      "fileid": "https://r2.ropensci.org/45cb851d6d06a46932c7f44645e2f9a7dd9bc5e2de35f90a644e7bae19c1ae2e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/41502849834"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.99.5",
      "date": "2026-11-02T18:47:43.000Z",
      "commit": "056ef164e484158823c2bb3b9d44009fb0dbb388",
      "fileid": "https://r2.ropensci.org/bc56971a6fc60031b24c7b2c05180d525475990dbbc4ca3c8c2f07c7d76e6ede",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/41502849834"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "0.99.5",
      "date": "2026-11-02T18:47:47.000Z",
      "commit": "056ef164e484158823c2bb3b9d44009fb0dbb388",
      "fileid": "https://r2.ropensci.org/4c35d22021690aeb4db2e306ebd6fbc6e2805b40156c5201f82f77e0b38efdbe",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/41502849834"
    }
  ]
}