{
  "_id": "6ace3ac6a14063b82c3b19d8",
  "Package": "ProActive",
  "Title": "Detect Elevations and Gaps in Mapped Sequencing Read Coverage",
  "Version": "0.1.0.9000",
  "Maintainer": "Jessie Maier <jlmaier@ncsu.edu>",
  "Authors@R": "c(person(given = \"Jessie\",\nfamily = \"Maier\",\nrole = c(\"aut\", \"cre\", \"cph\"),\nemail = \"jlmaier@ncsu.edu\",\ncomment = c(ORCID = \"0009-0001-8575-5386\")),\nperson(given = \"Manuel\",\nfamily = \"Kleiner\",\nrole= c(\"aut\", \"ths\"),\ncomment = c(ORCID = \"0000-0001-6904-0287\")))",
  "Description": "Automate the detection of gaps and elevations in mapped\nsequencing read coverage using a 2D pattern-matching algorithm.\n'ProActive' detects, characterizes and visualizes read coverage\npatterns in both genomes and metagenomes. Optionally, users may\nprovide gene annotations associated with their genome or\nmetagenome in the form of a .gff file. In this case,\n'ProActive' will generate an additional output table containing\nthe gene annotations found within the detected regions of\ngapped and elevated read coverage. Additionally, users can\nsearch for gene annotations of interest in the output read\ncoverage plots.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.2",
  "URL": "https://github.com/jlmaier12/ProActive,\nhttps://jlmaier12.github.io/ProActive/",
  "BugReports": "https://github.com/jlmaier12/ProActive/issues",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://jlmaier12.r-universe.dev",
  "Date/Publication": "2025-08-08 01:17:23 UTC",
  "RemoteUrl": "https://github.com/jlmaier12/proactive",
  "RemoteRef": "HEAD",
  "RemoteSha": "fe522fb8d5484bab74ce179a743e493596ee281b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-13 13:40:45 UTC",
    "User": "root"
  },
  "Author": "Jessie Maier [aut, cre, cph] (ORCID:\n<https://orcid.org/0009-0001-8575-5386>),\nManuel Kleiner [aut, ths] (ORCID:\n<https://orcid.org/0000-0001-6904-0287>)",
  "_user": "jlmaier12",
  "_type": "src",
  "_file": "ProActive_0.1.0.9000.tar.gz",
  "_fileid": "https://r2.ropensci.org/958d0f13582681ffafb04a40b16f394ffff4c295efc7197fa82423e52901cfac",
  "_filesize": 2740277,
  "_sha256": "958d0f13582681ffafb04a40b16f394ffff4c295efc7197fa82423e52901cfac",
  "_expires": "2027-01-21T14:05:52.000Z",
  "_created": "2026-10-13T13:40:45.000Z",
  "_published": "2026-10-13T14:05:58.593Z",
  "_buildurl": "https://github.com/r-universe/jlmaier12/actions/runs/38406415084",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 115329054037,
      "time": 186,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11818444188"
    },
    {
      "job": 115329054029,
      "time": 176,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11819500681"
    },
    {
      "job": 115329054206,
      "time": 158,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11821605587"
    },
    {
      "job": 115329054112,
      "time": 118,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11821450393"
    },
    {
      "job": 115327272959,
      "time": 221,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11819317824"
    },
    {
      "job": 115329053801,
      "time": 107,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11818543786"
    },
    {
      "job": 115329053940,
      "time": 176,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11819313728"
    },
    {
      "job": 115329054141,
      "time": 119,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11819670362"
    },
    {
      "job": 115329054269,
      "time": 124,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11818344526"
    }
  ],
  "_upstream": "https://github.com/jlmaier12/proactive",
  "_commit": {
    "id": "fe522fb8d5484bab74ce179a743e493596ee281b",
    "author": "jlmaier <jlmaier@ncsu.edu>",
    "committer": "jlmaier <jlmaier@ncsu.edu>",
    "message": "Start of development version, bug fixes and new gene annotation feature\n",
    "time": 1754615843
  },
  "_maintainer": {
    "name": "Jessie Maier",
    "email": "jlmaier@ncsu.edu",
    "login": "jlmaier12",
    "description": "",
    "uuid": 45083046,
    "orcid": "0009-0001-8575-5386"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.2.0",
      "role": "Depends"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "kableExtra",
      "role": "Suggests"
    }
  ],
  "_owner": "jlmaier12",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "bacteriophage",
    "metagenomics",
    "mobile-genetic-elements",
    "pattern-matching",
    "prophages",
    "read-mapping",
    "sequencing-coverage",
    "structural-variants",
    "transposable-elements"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "jlmaier12",
      "count": 41,
      "uuid": 45083046
    }
  ],
  "_userbio": {
    "uuid": 45083046,
    "type": "user",
    "name": "Jessie Maier",
    "followers": 1
  },
  "_downloads": {
    "count": 264,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ProActive"
  },
  "_devurl": "https://github.com/jlmaier12/proactive",
  "_pkgdown": "https://jlmaier12.github.io/ProActive/",
  "_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/NEWS.html",
    "extra/NEWS.txt",
    "extra/ProActive.html",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/jlmaier12/proactive",
  "_realowner": "jlmaier12",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.0.2",
      "date": "2025-01-17"
    },
    {
      "version": "0.1.0",
      "date": "2025-01-21"
    }
  ],
  "_exports": [
    "geneAnnotationSearch",
    "plotProActiveResults",
    "ProActiveDetect"
  ],
  "_datasets": [
    {
      "name": "sampleGenomegffTSV",
      "title": "sampleGenomegffTSV",
      "object": "sampleGenomegffTSV",
      "class": [
        "data.frame"
      ],
      "fields": [
        "V1",
        "V2",
        "V3",
        "V4",
        "V5",
        "V6",
        "V7",
        "V8",
        "V9"
      ],
      "rows": 85575,
      "table": true,
      "tojson": true
    },
    {
      "name": "sampleGenomePileup",
      "title": "sampleGenomePileup",
      "object": "sampleGenomePileup",
      "class": [
        "data.frame"
      ],
      "fields": [
        "V1",
        "V2",
        "V3",
        "V4"
      ],
      "rows": 48575,
      "table": true,
      "tojson": true
    },
    {
      "name": "sampleMetagenomegffTSV",
      "title": "sampleMetagenomegffTSV",
      "object": "sampleMetagenomegffTSV",
      "class": [
        "data.frame"
      ],
      "fields": [
        "V1",
        "V2",
        "V3",
        "V4",
        "V5",
        "V6",
        "V7",
        "V8",
        "V9"
      ],
      "rows": 470,
      "table": true,
      "tojson": true
    },
    {
      "name": "sampleMetagenomePileup",
      "title": "sampleMetagenomePileup",
      "object": "sampleMetagenomePileup",
      "class": [
        "data.frame"
      ],
      "fields": [
        "V1",
        "V2",
        "V3",
        "V4"
      ],
      "rows": 4604,
      "table": true,
      "tojson": true
    },
    {
      "name": "sampleMetagenomeResults",
      "title": "sampleMetagenomeResults",
      "object": "sampleMetagenomeResults",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "geneAnnotationSearch",
      "title": "Search for gene annotations on classified contigs/chunks",
      "topics": [
        "geneAnnotationSearch"
      ]
    },
    {
      "page": "plotProActiveResults",
      "title": "Plot results of `ProActive()` pattern-matching",
      "topics": [
        "plotProActiveResults"
      ]
    },
    {
      "page": "ProActiveDetect",
      "title": "Detect elevations and gaps in mapped read coverage patterns.",
      "topics": [
        "ProActiveDetect"
      ]
    }
  ],
  "_pkglogo": "https://github.com/jlmaier12/proactive/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/jlmaier12/proactive/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "dplyr",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "magrittr",
    "pillar",
    "pkgconfig",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "ProActiveVignette.Rmd",
      "filename": "ProActiveVignette.html",
      "title": "ProActive",
      "author": "Jessie Maier",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "CRAN install",
        "GitHub install",
        "Input data",
        "Pileups",
        "gff TSV",
        "ProActiveDetect()",
        "Function components",
        "Chunking",
        "Filtering",
        "Changing pileup windowSize",
        "Pattern-matching",
        "Elevation pattern:",
        "Gap pattern:",
        "Elevation/Gap pattern:",
        "noPattern:",
        "Calculating elevation ratios",
        "Extracting gene annotations in elevated/gapped regions",
        "Usage",
        "Arguments/parameters",
        "Output",
        "plotProActiveResults()",
        "Re-building pattern-matches",
        "Plotting read coverage and associated pattern-matches",
        "View select metagenome plots",
        "View select genome plots",
        "geneAnnotationSearch()",
        "Search for gene annotations",
        "Plot gene annotation locations",
        "Supplemental information",
        "Funding",
        "Session Information"
      ],
      "created": "2024-12-20 22:35:46",
      "modified": "2025-08-08 01:17:23",
      "commits": 7
    }
  ],
  "_score": 3.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "proactive",
  "_universes": [
    "jlmaier12"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.0.9000",
      "date": "2026-10-13T13:43:01.000Z",
      "distro": "resolute",
      "commit": "fe522fb8d5484bab74ce179a743e493596ee281b",
      "fileid": "https://r2.ropensci.org/211acd8e58e7aad5f3535094ace46cfc33eb0d0d4954d48103a71d70dd91c62d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jlmaier12/actions/runs/38406415084"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.0.9000",
      "date": "2026-10-13T13:42:57.000Z",
      "distro": "resolute",
      "commit": "fe522fb8d5484bab74ce179a743e493596ee281b",
      "fileid": "https://r2.ropensci.org/8e63401f27436c88ef97139b4c849ce561765f5bc2b44cb84af50e1d4334086b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jlmaier12/actions/runs/38406415084"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.0.9000",
      "date": "2026-10-13T14:04:21.000Z",
      "commit": "fe522fb8d5484bab74ce179a743e493596ee281b",
      "fileid": "https://r2.ropensci.org/cab269d609d89e8d86a845d3cf2e95da83d929c19750706439dfbf1a19c9ba9a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jlmaier12/actions/runs/38406415084"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.0.9000",
      "date": "2026-10-13T14:02:31.000Z",
      "commit": "fe522fb8d5484bab74ce179a743e493596ee281b",
      "fileid": "https://r2.ropensci.org/8e479e4c917ecf2000dc66970cec451bf9f4317708712807e910427c84bce976",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jlmaier12/actions/runs/38406415084"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.0.9000",
      "date": "2026-10-13T13:42:56.000Z",
      "commit": "fe522fb8d5484bab74ce179a743e493596ee281b",
      "fileid": "https://r2.ropensci.org/0d674d2a1b73e9a2e8a37479264ac427d181a6f0a7cce79e347707db75000cb5",
      "status": "success",
      "buildurl": "https://github.com/r-universe/jlmaier12/actions/runs/38406415084"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.0.9000",
      "date": "2026-10-13T13:42:42.000Z",
      "commit": "fe522fb8d5484bab74ce179a743e493596ee281b",
      "fileid": "https://r2.ropensci.org/77641cafb85c60e5c7a2e43cb1ab85d48366ff07bcb1bd6eb486ea38c410a02a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jlmaier12/actions/runs/38406415084"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.0.9000",
      "date": "2026-10-13T13:42:16.000Z",
      "commit": "fe522fb8d5484bab74ce179a743e493596ee281b",
      "fileid": "https://r2.ropensci.org/b5caa4d1e4ac5f24dca1e56dcfec2919c846b784b0e321b78bb911027b10d5dd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jlmaier12/actions/runs/38406415084"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.0.9000",
      "date": "2026-10-13T13:42:04.000Z",
      "commit": "fe522fb8d5484bab74ce179a743e493596ee281b",
      "fileid": "https://r2.ropensci.org/744f6ae0a8b5121e2932f5c36d5ca5c81a3975456d777b5b3ef20c7e3570bbc4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jlmaier12/actions/runs/38406415084"
    }
  ]
}