{
  "_id": "6a50c0ae89c83ec243a304c6",
  "Package": "KinSwingR",
  "Type": "Package",
  "Title": "KinSwingR: network-based kinase activity prediction",
  "Version": "1.31.0",
  "Authors@R": "person(\"Ashley J.\", \"Waardenberg\", email =\n\"a.waardenberg@gmail.com\", role=c(\"aut\", \"cre\"))",
  "Description": "KinSwingR integrates phosphosite data derived from\nmass-spectrometry data and kinase-substrate predictions to\npredict kinase activity. Several functions allow the user to\nbuild PWM models of kinase-subtrates, statistically infer\nPWM:substrate matches, and integrate these data to infer kinase\nactivity.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "biocViews": "Proteomics, SequenceMatching, Network",
  "RoxygenNote": "6.1.0",
  "VignetteBuilder": "knitr",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:48:53 UTC",
  "RemoteUrl": "https://github.com/bioc/KinSwingR",
  "RemoteRef": "HEAD",
  "RemoteSha": "b1c20f9c17a7eaf3a9ee1b22af3e648c380e02f2",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-10 09:46:42 UTC",
    "User": "root"
  },
  "Author": "Ashley J. Waardenberg [aut, cre]",
  "Maintainer": "Ashley J. Waardenberg <a.waardenberg@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "KinSwingR_1.31.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/3e4d1b1dd3ce739ab00ed4a8a9d71420395231a4dfa337afaba6fcebcbdd6200",
  "_filesize": 446776,
  "_sha256": "3e4d1b1dd3ce739ab00ed4a8a9d71420395231a4dfa337afaba6fcebcbdd6200",
  "_expires": "2026-10-18T09:51:41.000Z",
  "_created": "2026-07-10T09:46:42.000Z",
  "_published": "2026-07-10T09:51:42.752Z",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 13
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29083971835",
  "_status": "success",
  "_upstream": "https://github.com/bioc/KinSwingR",
  "_commit": {
    "id": "b1c20f9c17a7eaf3a9ee1b22af3e648c380e02f2",
    "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": 1777380533
  },
  "_maintainer": {
    "name": "Ashley J. Waardenberg",
    "email": "a.waardenberg@gmail.com",
    "login": "awaardenberg",
    "description": "",
    "uuid": 11515415
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 86333897710,
      "time": 144,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8224069541"
    },
    {
      "job": 86333897791,
      "time": 216,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8224096949"
    },
    {
      "job": 86333897969,
      "time": 262,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8224113409"
    },
    {
      "job": 86333897749,
      "time": 115,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8224059323"
    },
    {
      "job": 86333897910,
      "time": 121,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8224061402"
    },
    {
      "job": 86333239520,
      "time": 217,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8224016170"
    },
    {
      "job": 86333897822,
      "time": 115,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8224059339"
    },
    {
      "job": 86333897840,
      "time": 106,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8224056497"
    },
    {
      "job": 86333897844,
      "time": 118,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8224060481"
    },
    {
      "job": 86333897903,
      "time": 139,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8224068085"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "sqldf",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.31.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.30.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "proteomics",
    "sequencematching",
    "network"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 312,
    "source": "https://www.bioconductor.org/packages/stats/bioc/KinSwingR"
  },
  "_mentions": 1,
  "_searchresults": 7,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/KinSwingR.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "buildPWM",
    "cleanAnnotation",
    "scoreSequences",
    "swing",
    "viewPWM"
  ],
  "_datasets": [
    {
      "name": "example_phosphoproteome",
      "title": "Example phosphoproteome.",
      "object": "example_phosphoproteome",
      "class": [
        "data.frame"
      ],
      "fields": [
        "annotation",
        "peptide",
        "fc",
        "pval"
      ],
      "rows": 6215,
      "table": true,
      "tojson": true
    },
    {
      "name": "phosphositeplus_human",
      "title": "Human kinase-substrates derived from PhosphositePlus.",
      "object": "phosphositeplus_human",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "kinase",
        "substrate"
      ],
      "rows": 11985,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "buildPWM",
      "title": "Generate Position Weight Matrices (PWMs)",
      "topics": [
        "buildPWM"
      ]
    },
    {
      "page": "cleanAnnotation",
      "title": "Function for extracting peptide sequences from multimapped or complex annotated data",
      "topics": [
        "cleanAnnotation"
      ]
    },
    {
      "page": "example_phosphoproteome",
      "title": "Example phosphoproteome.",
      "topics": [
        "example_phosphoproteome"
      ]
    },
    {
      "page": "KinSwingR",
      "title": "KinSwingR: A package for predicting kinase activity",
      "topics": [
        "KinSwingR-package",
        "KinSwingR"
      ]
    },
    {
      "page": "phosphositeplus_human",
      "title": "Human kinase-substrates derived from PhosphositePlus.",
      "topics": [
        "phosphositeplus_human"
      ]
    },
    {
      "page": "scoreSequences",
      "title": "Score substrate sequences for matches to kinase Position Weight Matrices (PWMs)",
      "topics": [
        "scoreSequences"
      ]
    },
    {
      "page": "swing",
      "title": "Swing statistic",
      "topics": [
        "swing"
      ]
    },
    {
      "page": "viewPWM",
      "title": "View motif",
      "topics": [
        "viewPWM"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/KinSwingR/raw/HEAD/README.md",
  "_rundeps": [
    "BH",
    "BiocParallel",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "chron",
    "cli",
    "codetools",
    "cpp11",
    "data.table",
    "DBI",
    "fastmap",
    "formatR",
    "futile.logger",
    "futile.options",
    "glue",
    "gsubfn",
    "lambda.r",
    "lifecycle",
    "memoise",
    "pkgconfig",
    "proto",
    "rlang",
    "RSQLite",
    "snow",
    "sqldf",
    "vctrs"
  ],
  "_vignettes": [
    {
      "source": "KinSwingR.Rmd",
      "filename": "KinSwingR.html",
      "title": "KinSwingR: Predicting kinase activity from phosphoproteomics data",
      "author": "Ashley J. Waardenberg",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction to KinSwing",
        "KinSwingR example workflow",
        "Extracting peptides for analysis",
        "Build Position Weight Matrices (PWMs)",
        "Visualising motifs",
        "Score PWM matches against peptide sequences",
        "Predict kinase activity using swing()",
        "KinSwingR algorithm",
        "References"
      ],
      "created": "2018-09-21 02:26:33",
      "modified": "2019-04-30 05:31:33",
      "commits": 10
    }
  ],
  "_score": 4,
  "_indexed": true,
  "_nocasepkg": "kinswingr",
  "_universes": [
    "bioc",
    "awaardenberg"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-07-10T09:50:08.000Z",
      "distro": "resolute",
      "commit": "b1c20f9c17a7eaf3a9ee1b22af3e648c380e02f2",
      "fileid": "https://r2.ropensci.org/515d4316aa9ff9dd724fd45d0e6189e72116de51542bda42b48bb762288f6ed5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29083971835"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-07-10T09:50:55.000Z",
      "distro": "resolute",
      "commit": "b1c20f9c17a7eaf3a9ee1b22af3e648c380e02f2",
      "fileid": "https://r2.ropensci.org/b631ab42218e98665a30992d4cf8c836d81dfb2acf507410981920521d8f57c2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29083971835"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-07-10T09:48:35.000Z",
      "commit": "b1c20f9c17a7eaf3a9ee1b22af3e648c380e02f2",
      "fileid": "https://r2.ropensci.org/7f7403379f7360430867ceb263754076911b8558c590ede8804b2d36a4f825a2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29083971835"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-07-10T09:48:35.000Z",
      "commit": "b1c20f9c17a7eaf3a9ee1b22af3e648c380e02f2",
      "fileid": "https://r2.ropensci.org/e1dc0e5b932e682ebedd6ab114093e2975b85072efbbd136f183ee99dd2dffa7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29083971835"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.31.0",
      "date": "2026-07-10T09:48:52.000Z",
      "commit": "b1c20f9c17a7eaf3a9ee1b22af3e648c380e02f2",
      "fileid": "https://r2.ropensci.org/0d3b39ce88c4cc78a96d9171e7040ac7a8af56d229f6176d9602f97f4e36ac8b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29083971835"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-07-10T09:48:03.000Z",
      "commit": "b1c20f9c17a7eaf3a9ee1b22af3e648c380e02f2",
      "fileid": "https://r2.ropensci.org/df303efcbc57a1ee2f16479f18ff66b0ca2cea1e8f9f80fd53b4ccbfd7d488b9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29083971835"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-07-10T09:48:19.000Z",
      "commit": "b1c20f9c17a7eaf3a9ee1b22af3e648c380e02f2",
      "fileid": "https://r2.ropensci.org/b1991e5aa500aace7073fe5dc78b5afccc27c6034f1e5258bfc5d0ab049bd6cb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29083971835"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-07-10T09:48:39.000Z",
      "commit": "b1c20f9c17a7eaf3a9ee1b22af3e648c380e02f2",
      "fileid": "https://r2.ropensci.org/b736f131e8890cbb57d701bed26f89b744b69bc5cecbbc01a8cbbde0cc48148b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29083971835"
    }
  ]
}