{
  "_id": "6a494f1cf6c47c441949a52a",
  "Package": "DNAcycP2",
  "Title": "DNA Cyclizability Prediction",
  "Version": "1.5.1",
  "Authors@R": "c(\nperson(\"Brody\", \"Kendall\",\nemail = \"curtiskendall2025@u.northwestern.edu\",\nrole = \"aut\"),\nperson(\"Keren\", \"Li\",\nemail = \"kli@uab.edu\",\nrole = \"aut\"),\nperson(\"Ji-Ping\", \"Wang\",\nemail = \"jzwang@northwestern.edu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-8398-939X\")))",
  "Description": "This package performs prediction of intrinsic\ncyclizability of of every 50-bp subsequence in a DNA sequence.\nThe input could be a file either in FASTA or text format. The\noutput will be the C-score, the estimated intrinsic\ncyclizability score for each 50 bp sequences in each entry of\nthe sequence set.",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "StagedInstall": "yes",
  "biocViews": "NeuralNetwork, StructuralPrediction",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/jipingw/DNAcycP2",
  "BugReports": "https://github.com/jipingw/DNAcycP2",
  "Config/pak/sysreqs": "libpng-dev python3",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-02 23:13:24 UTC",
  "RemoteUrl": "https://github.com/bioc/DNAcycP2",
  "RemoteRef": "HEAD",
  "RemoteSha": "16bab4bfe395a365c81a2f62d907fecd2ec180f7",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-02 06:15:07 UTC",
    "User": "root"
  },
  "Author": "Brody Kendall [aut],\nKeren Li [aut],\nJi-Ping Wang [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-8398-939X>)",
  "Maintainer": "Ji-Ping Wang <jzwang@northwestern.edu>",
  "_user": "bioc",
  "_type": "src",
  "_file": "DNAcycP2_1.5.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/3d6901de04690379e247d52a4eddeab22f5a780cc94485b21516a38de44d2097",
  "_filesize": 2317755,
  "_sha256": "3d6901de04690379e247d52a4eddeab22f5a780cc94485b21516a38de44d2097",
  "_expires": "2026-10-12T18:21:14.000Z",
  "_created": "2026-07-02T06:15:07.000Z",
  "_published": "2026-07-04T18:21:16.100Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 2
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28568838332",
  "_status": "success",
  "_upstream": "https://github.com/bioc/DNAcycP2",
  "_commit": {
    "id": "16bab4bfe395a365c81a2f62d907fecd2ec180f7",
    "author": "Ji-Ping Wang <jzwang@northwestern.edu>",
    "committer": "Ji-Ping Wang <jzwang@northwestern.edu>",
    "message": "Fix DESCRIPTION and cycle_fasta.Rd during rebase\n",
    "time": 1777763604
  },
  "_maintainer": {
    "name": "Ji-Ping Wang",
    "email": "jzwang@northwestern.edu",
    "login": "jipingw",
    "description": "Professor in Statistics and Data Science, Adjunct Professor of Molecular BioSciences. My research interest is in interface of statistics and bi-medical sciences",
    "uuid": 45120092,
    "orcid": "0000-0002-8398-939X"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85155829386,
      "time": 154,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8030469372"
    },
    {
      "job": 85155829444,
      "time": 996,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8030711324"
    },
    {
      "job": 85155829337,
      "time": 961,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8030700884"
    },
    {
      "job": 85155829361,
      "time": 761,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8030644403"
    },
    {
      "job": 85155829395,
      "time": 535,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8030578337"
    },
    {
      "job": 85155829051,
      "time": 1074,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8030426718"
    },
    {
      "job": 85155829420,
      "time": 142,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8030466533"
    },
    {
      "job": 85155829300,
      "time": 235,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8030491597"
    },
    {
      "job": 85155829447,
      "time": 230,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8030490474"
    },
    {
      "job": 85155829355,
      "time": 258,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8030498608"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4.0",
      "role": "Depends"
    },
    {
      "package": "basilisk",
      "role": "Imports"
    },
    {
      "package": "reticulate",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "tinytest",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "Biostrings",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 3
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.5.1",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.4.1",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "neuralnetwork",
    "structuralprediction"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "jipingw",
      "count": 33,
      "uuid": 45120092
    },
    {
      "user": "jwokaty",
      "count": 6,
      "uuid": 1744257
    },
    {
      "user": "js2264",
      "count": 4,
      "uuid": 19528818
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 444,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://github.com/jipingw/dnacycp2",
  "_searchresults": 3,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/DNAcycP2.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/jipingw/dnacycp2",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "cycle",
    "cycle_fasta"
  ],
  "_help": [
    {
      "page": "cycle",
      "title": "Predict Cyclizability",
      "topics": [
        "cycle"
      ]
    },
    {
      "page": "cycle_fasta",
      "title": "Predict Cyclizability",
      "topics": [
        "cycle_fasta"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/DNAcycP2/raw/HEAD/README.md",
  "_rundeps": [
    "basilisk",
    "dir.expiry",
    "filelock",
    "here",
    "jsonlite",
    "lattice",
    "Matrix",
    "png",
    "rappdirs",
    "Rcpp",
    "RcppTOML",
    "reticulate",
    "rlang",
    "rprojroot",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "dnacycp2.Rmd",
      "filename": "dnacycp2.html",
      "title": "DNAcycP2: DNA Cyclizability Prediction v2",
      "author": "Brody Kendall, Ji-Ping Wang, and Keren Li",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Key differences between DNAcycP2 and DNAcycP",
        "Available formats of DNAcycP2 and DNAcycP",
        "Installation",
        "Usage",
        "Main Functions",
        "Selecting the Prediction Model",
        "Parallelization with cycle_fasta",
        "Example 1: fasta file input",
        "Example 2: input as a list/vector of sequences",
        "DNAcycP2 prediction -- Normalized vs unnormalized",
        "Save DNAcycP2 prediciton to external file",
        "Example 3 (Single Sequence):",
        "Example 4: DNAStringSet object input",
        "References",
        "Session info"
      ],
      "created": "2025-01-23 16:42:26",
      "modified": "2025-03-12 11:34:28",
      "commits": 6
    }
  ],
  "_score": 4.301029995663981,
  "_indexed": true,
  "_nocasepkg": "dnacycp2",
  "_universes": [
    "bioc",
    "jipingw"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.5.1",
      "date": "2026-07-02T06:17:43.000Z",
      "distro": "resolute",
      "commit": "16bab4bfe395a365c81a2f62d907fecd2ec180f7",
      "fileid": "https://r2.ropensci.org/373a65c967eb37c33f212368c9e2ecbcc9643cd88a5b3c4d956fa23afa1da0a1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28568838332"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.5.1",
      "date": "2026-07-02T06:17:40.000Z",
      "distro": "resolute",
      "commit": "16bab4bfe395a365c81a2f62d907fecd2ec180f7",
      "fileid": "https://r2.ropensci.org/4ab590c078d195537262b5f8388b074971240726beef2535d2d472dcd9c82618",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28568838332"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.5.1",
      "date": "2026-07-02T06:16:50.000Z",
      "commit": "16bab4bfe395a365c81a2f62d907fecd2ec180f7",
      "fileid": "https://r2.ropensci.org/7d5d0dd5b78c1fef2e5a9192f142b3686c514ced0ada60e8833f98ea66599226",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28568838332"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.5.1",
      "date": "2026-07-02T06:16:30.000Z",
      "commit": "16bab4bfe395a365c81a2f62d907fecd2ec180f7",
      "fileid": "https://r2.ropensci.org/7099ecc0d57ffa3c0edf0ed2be1789c906992b6725711085fb26803c4b5ce078",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28568838332"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.5.1",
      "date": "2026-07-02T06:17:49.000Z",
      "commit": "16bab4bfe395a365c81a2f62d907fecd2ec180f7",
      "fileid": "https://r2.ropensci.org/05e1fca629a20739db36d94c0f6688e3c69a2bdc0f9954e850ba66a2b7c2320e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28568838332"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.5.1",
      "date": "2026-07-02T06:16:25.000Z",
      "commit": "16bab4bfe395a365c81a2f62d907fecd2ec180f7",
      "fileid": "https://r2.ropensci.org/1fd93ef8c8a318a5959522b8305ba831bd35dd9686f73c709510f6e4b32bc120",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28568838332"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.5.1",
      "date": "2026-07-02T06:16:21.000Z",
      "commit": "16bab4bfe395a365c81a2f62d907fecd2ec180f7",
      "fileid": "https://r2.ropensci.org/7e88a5917bba311d31cf45d673f36df935d3e2ece8bf6d50a386bc2b735aaa1f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28568838332"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.5.1",
      "date": "2026-07-02T06:16:36.000Z",
      "commit": "16bab4bfe395a365c81a2f62d907fecd2ec180f7",
      "fileid": "https://r2.ropensci.org/b3d34ddc1bef0d6dd73bfd20cbadfc7bac1ca2c1bc36495ecb8e137fe28daad6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28568838332"
    }
  ]
}