{ "_id": "6a214116cd65a98ecbd2a5d2", "Package": "ProActive", "Title": "Detect Elevations and Gaps in Mapped Sequencing Read Coverage", "Version": "0.1.0.9000", "Maintainer": "Jessie Maier ", "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": "2026-06-04 09:06:28 UTC", "User": "root" }, "Author": "Jessie Maier [aut, cre, cph] (ORCID:\n),\nManuel Kleiner [aut, ths] (ORCID:\n)", "MD5sum": "f835dd6b1b2c42bd9591fc8e74bb65aa", "_user": "jlmaier12", "_type": "src", "_file": "ProActive_0.1.0.9000.tar.gz", "_fileid": "aedeb7cc1a9f6d7158b58f307262d36b6a6a00968069cf54940340c3d2e872e7", "_filesize": 2743475, "_sha256": "aedeb7cc1a9f6d7158b58f307262d36b6a6a00968069cf54940340c3d2e872e7", "_created": "2026-06-04T09:06:28.000Z", "_published": "2026-06-04T09:10:46.120Z", "_distro": "noble", "_jobs": [ { "job": 79486101206, "time": 186, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7407492962" }, { "job": 79486101178, "time": 162, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7407484748" }, { "job": 79486101326, "time": 218, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7407491532" }, { "job": 79486101438, "time": 217, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7407492729" }, { "job": 79485312172, "time": 289, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7407427293" }, { "job": 79486101175, "time": 118, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7407469652" }, { "job": 79486101214, "time": 171, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7407488449" }, { "job": 79486101339, "time": 170, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7407487807" }, { "job": 79486101433, "time": 162, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7407484812" } ], "_buildurl": "https://github.com/r-universe/jlmaier12/actions/runs/26941895244", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/jlmaier12/proactive", "_commit": { "id": "fe522fb8d5484bab74ce179a743e493596ee281b", "author": "jlmaier ", "committer": "jlmaier ", "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 }, "_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": [ { "week": "2025-32", "n": 1 } ], "_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" }, "_downloads": { "count": 105, "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": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/ProActive.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_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": "2026-06-04T09:08:48.000Z", "distro": "noble", "commit": "fe522fb8d5484bab74ce179a743e493596ee281b", "fileid": "af472d52ead275ff6f9c09b7264adfc2a600f502ce0740f127d5acd67d7401bc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jlmaier12/actions/runs/26941895244" }, { "r": "4.6.0", "os": "linux", "version": "0.1.0.9000", "date": "2026-06-04T09:08:30.000Z", "distro": "noble", "commit": "fe522fb8d5484bab74ce179a743e493596ee281b", "fileid": "4842923bcdef73fc38dc582767ee7ca6423f1373b36be81359bce2fbc514f0d0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jlmaier12/actions/runs/26941895244" }, { "r": "4.5.3", "os": "mac", "version": "0.1.0.9000", "date": "2026-06-04T09:09:00.000Z", "commit": "fe522fb8d5484bab74ce179a743e493596ee281b", "fileid": "004ce8a2564c5771583c2a1b4ef688908886d31c682881639a08dd5b8e14ad24", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jlmaier12/actions/runs/26941895244" }, { "r": "4.6.0", "os": "mac", "version": "0.1.0.9000", "date": "2026-06-04T09:09:04.000Z", "commit": "fe522fb8d5484bab74ce179a743e493596ee281b", "fileid": "b54c068f21e5aa2513c2b1a9e1974230db1c972cb00bc78662cf54f5e535dd89", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jlmaier12/actions/runs/26941895244" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.0.9000", "date": "2026-06-04T09:08:45.000Z", "commit": "fe522fb8d5484bab74ce179a743e493596ee281b", "fileid": "17388e1bc4c26a59b65993f308fe2dc23cf40752cec427e48e2e7bd54d4685a4", "status": "success", "buildurl": "https://github.com/r-universe/jlmaier12/actions/runs/26941895244" }, { "r": "4.7.0", "os": "win", "version": "0.1.0.9000", "date": "2026-06-04T09:08:08.000Z", "commit": "fe522fb8d5484bab74ce179a743e493596ee281b", "fileid": "5e52d2e29d3396fdd5263c0c94f7cf43cb4c64a1cd4f471fec123b5dadebd824", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jlmaier12/actions/runs/26941895244" }, { "r": "4.5.3", "os": "win", "version": "0.1.0.9000", "date": "2026-06-04T09:08:12.000Z", "commit": "fe522fb8d5484bab74ce179a743e493596ee281b", "fileid": "da66d665e06cb2a87e0a31dccf738af0c188b3f04809a2ca34f5f48f670164d6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jlmaier12/actions/runs/26941895244" }, { "r": "4.6.0", "os": "win", "version": "0.1.0.9000", "date": "2026-06-04T09:07:57.000Z", "commit": "fe522fb8d5484bab74ce179a743e493596ee281b", "fileid": "b51ba49dce4cfb3221302d693f886f015f04b90cd9c5deede20dbd174e2d6d8e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jlmaier12/actions/runs/26941895244" } ] }