{
  "_id": "6a1ac1d71d7bb097a09d8d51",
  "Package": "periodicDNA",
  "Type": "Package",
  "Title": "Set of tools to identify periodic occurrences of k-mers in DNA\nsequences",
  "Version": "1.23.0",
  "Date": "2025-07-24",
  "Encoding": "UTF-8",
  "Authors@R": "c(person(given = \"Jacques\",\nfamily = \"Serizay\",\nrole = c(\"aut\", \"cre\"),\nemail = \"jacquesserizay@gmail.com\",\ncomment = c(ORCID = \"0000-0002-4295-0624\")))",
  "Description": "This R package helps the user identify k-mers (e.g. di- or\ntri-nucleotides) present periodically in a set of genomic loci\n(typically regulatory elements). The functions of this package\nprovide a straightforward approach to find periodic occurrences\nof k-mers in DNA sequences, such as regulatory elements. It is\nnot aimed at identifying motifs separated by a conserved\ndistance; for this type of analysis, please visit MEME website.",
  "URL": "https://github.com/js2264/periodicDNA",
  "BugReports": "https://github.com/js2264/periodicDNA/issues",
  "RoxygenNote": "7.1.0",
  "VignetteBuilder": "knitr",
  "biocViews": "SequenceMatching, MotifDiscovery, MotifAnnotation,\nSequencing, Coverage, Alignment, DataImport",
  "License": "GPL-3 + file LICENSE",
  "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:53:34 UTC",
  "RemoteUrl": "https://github.com/bioc/periodicDNA",
  "RemoteRef": "HEAD",
  "RemoteSha": "e77802fa374d97a376a36a23fa6804ef2698791b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 07:30:05 UTC",
    "User": "root"
  },
  "Author": "Jacques Serizay [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-4295-0624>)",
  "Maintainer": "Jacques Serizay <jacquesserizay@gmail.com>",
  "MD5sum": "5d1e988da700e3f62563df53a533089f",
  "_user": "bioc",
  "_type": "src",
  "_file": "periodicDNA_1.23.0.tar.gz",
  "_fileid": "dd1f0d6ac550b4040bdb7abbd3fc3a1c4c3190a1832f9959c7686329f483b5ce",
  "_filesize": 3386899,
  "_sha256": "dd1f0d6ac550b4040bdb7abbd3fc3a1c4c3190a1832f9959c7686329f483b5ce",
  "_created": "2026-05-30T07:30:05.000Z",
  "_published": "2026-05-30T10:54:15.792Z",
  "_jobs": [
    {
      "job": 78633649393,
      "time": 421,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306530269"
    },
    {
      "job": 78633649407,
      "time": 653,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7306553602"
    },
    {
      "job": 78633649388,
      "time": 666,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7306555027"
    },
    {
      "job": 78633649397,
      "time": 331,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7307631488"
    },
    {
      "job": 78633649410,
      "time": 320,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307621237"
    },
    {
      "job": 78633212788,
      "time": 468,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306484413"
    },
    {
      "job": 78633649386,
      "time": 334,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306521469"
    },
    {
      "job": 78633649419,
      "time": 455,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7306533881"
    },
    {
      "job": 78633649412,
      "time": 550,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7306543143"
    },
    {
      "job": 78633649427,
      "time": 487,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7306536795"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 8
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677964889",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/periodicDNA",
  "_commit": {
    "id": "e77802fa374d97a376a36a23fa6804ef2698791b",
    "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": 1777380814
  },
  "_maintainer": {
    "name": "Jacques Serizay",
    "email": "jacquesserizay@gmail.com",
    "login": "js2264",
    "description": "work <- think() |>\n  code() |> \n  tidy() |> \n  write()",
    "uuid": 19528818,
    "orcid": "0000-0002-4295-0624"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "Biostrings",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "role": "Depends"
    },
    {
      "package": "IRanges",
      "role": "Depends"
    },
    {
      "package": "BSgenome",
      "role": "Depends"
    },
    {
      "package": "BiocParallel",
      "role": "Depends"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "zoo",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "cowplot",
      "role": "Imports"
    },
    {
      "package": "BSgenome.Scerevisiae.UCSC.sacCer3",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Celegans.UCSC.ce11",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Dmelanogaster.UCSC.dm6",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Drerio.UCSC.danRer10",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Hsapiens.UCSC.hg38",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Mmusculus.UCSC.mm10",
      "role": "Suggests"
    },
    {
      "package": "reticulate",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "pkgdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-30",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.23.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.22.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "sequencematching",
    "motifdiscovery",
    "motifannotation",
    "sequencing",
    "coverage",
    "alignment",
    "dataimport"
  ],
  "_stars": 6,
  "_contributors": [
    {
      "user": "js2264",
      "count": 9,
      "uuid": 19528818
    },
    {
      "user": "nturaga",
      "count": 8,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 2,
      "uuid": 1744257
    },
    {
      "user": "hpages",
      "count": 1,
      "uuid": 8810451
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 376,
    "source": "https://www.bioconductor.org/packages/stats/bioc/periodicDNA"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/js2264/periodicdna",
  "_searchresults": 5,
  "_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/periodicDNA.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/js2264/periodicdna",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "getPeriodicity",
    "getPeriodicityTrack",
    "getPeriodicityWithIterations",
    "plotAggregateCoverage",
    "plotPeriodicityResults",
    "setUpBPPARAM",
    "theme_ggplot2"
  ],
  "_datasets": [
    {
      "name": "ce11_all_REs",
      "title": "ce11_all_REs",
      "object": "ce11_all_REs",
      "file": "ce11_all_REs.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ce11_ATACseq",
      "title": "ce11_ATACseq",
      "object": "ce11_ATACseq",
      "file": "ce11_ATACseq.rda",
      "class": [
        "SimpleRleList"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ce11_proms",
      "title": "ce11_proms",
      "object": "ce11_proms",
      "file": "ce11_proms.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ce11_proms_seqs",
      "title": "ce11_proms_seqs",
      "object": "ce11_proms_seqs",
      "file": "ce11_proms_seqs.rda",
      "class": [
        "DNAStringSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ce11_TSSs",
      "title": "ce11_TSSs",
      "object": "ce11_TSSs",
      "file": "ce11_TSSs.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ce11_WW_10bp",
      "title": "ce11_WW_10bp",
      "object": "ce11_WW_10bp",
      "file": "ce11_WW_10bp.rda",
      "class": [
        "SimpleRleList"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "ce11_all_REs",
      "title": "ce11_all_REs",
      "topics": [
        "ce11_all_REs"
      ]
    },
    {
      "page": "ce11_ATACseq",
      "title": "ce11_ATACseq",
      "topics": [
        "ce11_ATACseq"
      ]
    },
    {
      "page": "ce11_proms",
      "title": "ce11_proms",
      "topics": [
        "ce11_proms"
      ]
    },
    {
      "page": "ce11_proms_seqs",
      "title": "ce11_proms_seqs",
      "topics": [
        "ce11_proms_seqs"
      ]
    },
    {
      "page": "ce11_TSSs",
      "title": "ce11_TSSs",
      "topics": [
        "ce11_TSSs"
      ]
    },
    {
      "page": "ce11_WW_10bp",
      "title": "ce11_WW_10bp",
      "topics": [
        "ce11_WW_10bp"
      ]
    },
    {
      "page": "getPeriodicity",
      "title": "A function to compute k-mer periodicity in sequence(s).",
      "topics": [
        "getPeriodicity",
        "getPeriodicity.DNAString",
        "getPeriodicity.DNAStringSet",
        "getPeriodicity.GRanges"
      ]
    },
    {
      "page": "getPeriodicityTrack",
      "title": "Function to generate a k-mer periodicity track",
      "topics": [
        "getPeriodicityTrack"
      ]
    },
    {
      "page": "getPeriodicityWithIterations",
      "title": "A function to compute PSDs with iterations",
      "topics": [
        "getPeriodicityWithIterations",
        "getPeriodicityWithIterations.DNAStringSet",
        "getPeriodicityWithIterations.GRanges"
      ]
    },
    {
      "page": "plotAggregateCoverage",
      "title": "A function to plot aggregated signals over sets of GRanges",
      "topics": [
        "plotAggregateCoverage",
        "plotAggregateCoverage.CompressedRleList",
        "plotAggregateCoverage.list",
        "plotAggregateCoverage.SimpleRleList"
      ]
    },
    {
      "page": "plotPeriodicityResults",
      "title": "Plot the output of getPeriodicity()",
      "topics": [
        "plotPeriodicityResults"
      ]
    },
    {
      "page": "setUpBPPARAM",
      "title": "setUpBPPARAM",
      "topics": [
        "setUpBPPARAM"
      ]
    },
    {
      "page": "theme_ggplot2",
      "title": "Personal ggplot2 theming function, adapted from roboto-condensed at https://github.com/hrbrmstr/hrbrthemes/",
      "topics": [
        "theme_ggplot2"
      ]
    }
  ],
  "_pkglogo": "https://github.com/bioc/periodicDNA/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/bioc/periodicDNA/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "BSgenome",
    "cigarillo",
    "cli",
    "codetools",
    "cowplot",
    "cpp11",
    "crayon",
    "curl",
    "DelayedArray",
    "farver",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "httr",
    "IRanges",
    "isoband",
    "jsonlite",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mime",
    "openssl",
    "R6",
    "RColorBrewer",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "sys",
    "vctrs",
    "viridisLite",
    "withr",
    "XML",
    "XVector",
    "yaml",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "periodicDNA.Rmd",
      "filename": "periodicDNA.html",
      "title": "periodicDNA",
      "author": "Jacques Serizay",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction to periodicDNA",
        "Internal steps of periodicDNA",
        "Quantifying k-mer periodicity over a set of sequences",
        "Basic usage",
        "Repeated shuffling of input sequences",
        "Note",
        "Track of periodicity over a set of Genomic Ranges",
        "Session info"
      ],
      "created": "2020-05-04 17:44:10",
      "modified": "2020-09-07 08:03:00",
      "commits": 26
    }
  ],
  "_score": 5.431363764158988,
  "_indexed": true,
  "_nocasepkg": "periodicdna",
  "_universes": [
    "bioc",
    "js2264"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-05-30T07:37:25.000Z",
      "distro": "noble",
      "commit": "e77802fa374d97a376a36a23fa6804ef2698791b",
      "fileid": "9e035926ac918393053252018dd6ea249dd701bf7625d432b3e742a938533f73",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677964889"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-05-30T07:37:34.000Z",
      "distro": "noble",
      "commit": "e77802fa374d97a376a36a23fa6804ef2698791b",
      "fileid": "1e03018b3e6ae11ede28d762918c7f938531353b187795b8df3acef707f197e2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677964889"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-05-30T10:46:34.000Z",
      "commit": "e77802fa374d97a376a36a23fa6804ef2698791b",
      "fileid": "fc57cf1a4c9bc63020d4950f3cd5336505e32256e9f7370ee72bdea996015f45",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677964889"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-05-30T10:44:43.000Z",
      "commit": "e77802fa374d97a376a36a23fa6804ef2698791b",
      "fileid": "6ae5fb34bfc1d027c2f110998c7aa9cdb2b4b74307da4e9613fc0ddfbef84705",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677964889"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.23.0",
      "date": "2026-05-30T07:36:19.000Z",
      "commit": "e77802fa374d97a376a36a23fa6804ef2698791b",
      "fileid": "b5596d07f7263e56cc4ae58138f5fe50e6bdf34d8d6e5b0d53622066ede7fc6b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677964889"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-05-30T07:35:00.000Z",
      "commit": "e77802fa374d97a376a36a23fa6804ef2698791b",
      "fileid": "37639bf60c2eaad54dad5b2084fc5c558e5d42ff748883a1b958dce167fb2e6d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677964889"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-05-30T07:35:27.000Z",
      "commit": "e77802fa374d97a376a36a23fa6804ef2698791b",
      "fileid": "dd6484a0f6a4e6dd0fb53824f05e2d8c68aeda9ea0219c3b62a7321a334ea2d8",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677964889"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-05-30T07:34:15.000Z",
      "commit": "e77802fa374d97a376a36a23fa6804ef2698791b",
      "fileid": "44d4c811066bcce3fb4a21252ea5f81301b6607ce63b6cbb8afaca483599fad2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677964889"
    }
  ]
}