{
  "_id": "6acb62a4fe5cc25786e8f1f3",
  "Package": "wavFeatExt",
  "Type": "Package",
  "Title": "Wavelet-based Feature Extraction for Copy-number Alteration Data",
  "Version": "1.1.0",
  "Authors@R": "c(\nperson(\"Maharani Ahsani\", \"Ummi\",\nemail = \"maharaniahsani@itb.ac.id\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Arief\", \"Gusnanto\",\nrole = \"aut\")\n)",
  "Description": "Provides tools for simulating copy-number alteration (CNA)\nprofiles, applying a non-decimated Haar wavelet transform to\ngenomic signals, and extracting wavelet-derived features for\nuse in supervised learning. Multiple machine learning methods\nincluding lasso and elastic-net regularisation, random forest,\npartial least squares, neural networks and k-nearest neighbours\nare implemented to train predictive models from genomic feature\nvectors. The workflow enables end-to-end analysis from CNA\nsimulation to feature extraction and classification.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "biocViews": "CopyNumberVariation, GenomicVariation, FeatureExtraction,\nClassification,",
  "URL": "https://github.com/maharaniau/wavFeatExt",
  "BugReports": "https://github.com/maharaniau/wavFeatExt/issues",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:07:13 UTC",
  "RemoteUrl": "https://github.com/bioc/wavFeatExt",
  "RemoteRef": "HEAD",
  "RemoteSha": "62f26cb7ae4946b720e082819bfad3ac9ed73a3d",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-11 09:54:13 UTC",
    "User": "root"
  },
  "Author": "Maharani Ahsani Ummi [aut, cre],\nArief Gusnanto [aut]",
  "Maintainer": "Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>",
  "_user": "bioc",
  "_type": "src",
  "_file": "wavFeatExt_1.1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/eb227401ac2fb64bf1f8409ea46c3946e4039db59a10a77728a7562421014855",
  "_filesize": 448071,
  "_sha256": "eb227401ac2fb64bf1f8409ea46c3946e4039db59a10a77728a7562421014855",
  "_expires": "2027-01-19T10:19:14.000Z",
  "_created": "2026-10-11T09:54:13.000Z",
  "_published": "2026-10-11T10:19:16.656Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38129802463",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 4
  },
  "_upstream": "https://github.com/bioc/wavFeatExt",
  "_commit": {
    "id": "62f26cb7ae4946b720e082819bfad3ac9ed73a3d",
    "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": 1777381633
  },
  "_maintainer": {
    "name": "Maharani Ahsani Ummi",
    "email": "maharaniahsani@itb.ac.id"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 114442308883,
      "time": 157,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11698717158"
    },
    {
      "job": 114442308945,
      "time": 190,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11698928256"
    },
    {
      "job": 114442308911,
      "time": 272,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11698438969"
    },
    {
      "job": 114442308901,
      "time": 115,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11698244320"
    },
    {
      "job": 114442308882,
      "time": 145,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11698139331"
    },
    {
      "job": 114441652488,
      "time": 226,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11698242416"
    },
    {
      "job": 114442308887,
      "time": 98,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11698843225"
    },
    {
      "job": 114442308924,
      "time": 108,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11698523662"
    },
    {
      "job": 114442308929,
      "time": 111,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11698527333"
    },
    {
      "job": 114442308935,
      "time": 107,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11697959787"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5",
      "role": "Depends"
    },
    {
      "package": "DNAcopy",
      "role": "Imports"
    },
    {
      "package": "wavethresh",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "randomForest",
      "role": "Imports"
    },
    {
      "package": "glmnet",
      "role": "Imports"
    },
    {
      "package": "pROC",
      "role": "Imports"
    },
    {
      "package": "neuralnet",
      "role": "Imports"
    },
    {
      "package": "e1071",
      "role": "Imports"
    },
    {
      "package": "class",
      "role": "Imports"
    },
    {
      "package": "caret",
      "role": "Imports"
    },
    {
      "package": "ica",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "pls",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-03",
      "n": 2
    },
    {
      "week": "2026-04",
      "n": 2
    },
    {
      "week": "2026-05",
      "n": 2
    },
    {
      "week": "2026-08",
      "n": 6
    },
    {
      "week": "2026-10",
      "n": 1
    },
    {
      "week": "2026-11",
      "n": 14
    },
    {
      "week": "2026-14",
      "n": 2
    },
    {
      "week": "2026-15",
      "n": 7
    },
    {
      "week": "2026-16",
      "n": 4
    },
    {
      "week": "2026-17",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.1.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.0.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "copynumbervariation",
    "genomicvariation",
    "featureextraction",
    "classification"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "maharaniau",
      "count": 6,
      "uuid": 94630089
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 476,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 281,
    "source": "https://www.bioconductor.org/packages/stats/bioc/wavFeatExt"
  },
  "_devurl": "https://github.com/maharaniau/wavfeatext",
  "_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/wavFeatExt.html"
  ],
  "_homeurl": "https://github.com/maharaniau/wavfeatext",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "CBS",
    "classifyPcaIca",
    "classifyWavFeatExt",
    "getIca",
    "getPca",
    "nhwt",
    "seg",
    "simulateCNA",
    "wavFeatExt"
  ],
  "_help": [
    {
      "page": "CBS",
      "title": "Circular Binary Segmentation of Copy-number Profiles",
      "topics": [
        "CBS"
      ]
    },
    {
      "page": "classifyPcaIca",
      "title": "Classification on PCA- and ICA-based Feature Sets",
      "topics": [
        "classifyPcaIca"
      ]
    },
    {
      "page": "classifyWavFeatExt",
      "title": "Classification on Wavelet-based Features",
      "topics": [
        "classifyWavFeatExt"
      ]
    },
    {
      "page": "getIca",
      "title": "Independent Component Analysis (ICA) for a List of Matrices",
      "topics": [
        "getIca"
      ]
    },
    {
      "page": "getPca",
      "title": "Principal Component Analysis (PCA) for a List of Matrices",
      "topics": [
        "getPca"
      ]
    },
    {
      "page": "nhwt",
      "title": "Non-decimated Haar Wavelet Transform (Legacy)",
      "topics": [
        "nhwt"
      ]
    },
    {
      "page": "plot.nhwt",
      "title": "Plot non-decimated Haar wavelet transform coefficients",
      "topics": [
        "plot.nhwt"
      ]
    },
    {
      "page": "plot.pcaIcaClassifier",
      "title": "Plot Classification Results from 'classifyPcaIca'",
      "topics": [
        "plot.pcaIcaClassifier"
      ]
    },
    {
      "page": "plot.wavFeatExtClassifier",
      "title": "Plot Classification Results from 'classifyWavFeatExt'",
      "topics": [
        "plot.wavFeatExtClassifier"
      ]
    },
    {
      "page": "seg",
      "title": "Segmentation Per Observation Using CBS",
      "topics": [
        "seg"
      ]
    },
    {
      "page": "simulateCNA",
      "title": "Simulate Copy-number Alteration (CNA) Data in a Two-group Setting",
      "topics": [
        "simulateCNA"
      ]
    },
    {
      "page": "wavFeatExt",
      "title": "Feature Extraction Using Non-decimated Haar Wavelet Transform",
      "topics": [
        "wavFeatExt"
      ]
    }
  ],
  "_rundeps": [
    "caret",
    "class",
    "cli",
    "clock",
    "codetools",
    "cpp11",
    "data.table",
    "Deriv",
    "diagram",
    "digest",
    "DNAcopy",
    "dplyr",
    "e1071",
    "farver",
    "foreach",
    "future",
    "future.apply",
    "generics",
    "ggplot2",
    "glmnet",
    "globals",
    "glue",
    "gower",
    "gtable",
    "hardhat",
    "ica",
    "ipred",
    "isoband",
    "iterators",
    "KernSmooth",
    "labeling",
    "lattice",
    "lava",
    "lifecycle",
    "listenv",
    "lubridate",
    "magrittr",
    "MASS",
    "Matrix",
    "matrixStats",
    "ModelMetrics",
    "neuralnet",
    "nlme",
    "nnet",
    "numDeriv",
    "parallelly",
    "pillar",
    "pkgconfig",
    "pls",
    "plyr",
    "pROC",
    "prodlim",
    "progressr",
    "proxy",
    "purrr",
    "R6",
    "randomForest",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "recipes",
    "reshape2",
    "rlang",
    "rpart",
    "S7",
    "scales",
    "shape",
    "sparsevctrs",
    "SQUAREM",
    "stringi",
    "stringr",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "timechange",
    "timeDate",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "wavethresh",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "wavFeatExt.Rmd",
      "filename": "wavFeatExt.html",
      "title": "wavFeatExt: Wavelet-based Feature Extraction for Copy-number Alteration Data",
      "author": "Maharani Ahsani Ummi, Arief Gusnanto",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Getting Started",
        "Input data structure",
        "Simulation",
        "Simulating CNA data",
        "Wavelet-based feature extraction",
        "Visualising wavelet coefficients for a single profile",
        "Classification using wavelet features",
        "Comparison with PCA/ICA",
        "Plotting classification error and AUC",
        "Session Information"
      ],
      "created": "2026-04-02 08:10:17",
      "modified": "2026-04-20 02:59:22",
      "commits": 4
    }
  ],
  "_score": 4.041392685158225,
  "_indexed": true,
  "_nocasepkg": "wavfeatext",
  "_universes": [
    "bioc",
    "maharaniau"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-10-11T09:56:54.000Z",
      "distro": "resolute",
      "commit": "62f26cb7ae4946b720e082819bfad3ac9ed73a3d",
      "fileid": "https://r2.ropensci.org/d9794f05a23d982ea1927cb123c781e392b8b6c4a820cfc7b1bcb449df91554f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38129802463"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-10-11T09:58:12.000Z",
      "distro": "resolute",
      "commit": "62f26cb7ae4946b720e082819bfad3ac9ed73a3d",
      "fileid": "https://r2.ropensci.org/539ba794f6194a7d30f7cb701ba0fea0c6f735554d7a279631517a72cc97f2c9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38129802463"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-10-11T10:18:18.000Z",
      "commit": "62f26cb7ae4946b720e082819bfad3ac9ed73a3d",
      "fileid": "https://r2.ropensci.org/b03d06993dc63da5ba183f6084e5e9dbecfdd54e78bca03df086ddef42a41b1a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38129802463"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-10-11T10:17:23.000Z",
      "commit": "62f26cb7ae4946b720e082819bfad3ac9ed73a3d",
      "fileid": "https://r2.ropensci.org/1247e0b95c758288a6564a6312266e3d62c87ab0d789d43b77d45392e39ae87a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38129802463"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.0",
      "date": "2026-10-11T09:56:15.000Z",
      "commit": "62f26cb7ae4946b720e082819bfad3ac9ed73a3d",
      "fileid": "https://r2.ropensci.org/4522901334d9d12506eccb3b0a82bc2f696adf4970a7018a8d92f801a3f31117",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38129802463"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-10-11T09:55:33.000Z",
      "commit": "62f26cb7ae4946b720e082819bfad3ac9ed73a3d",
      "fileid": "https://r2.ropensci.org/827fa35764a39635268e2f0cacbbb2d7e024ee4e3468a8037744bebea7f01e05",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38129802463"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-10-11T09:55:45.000Z",
      "commit": "62f26cb7ae4946b720e082819bfad3ac9ed73a3d",
      "fileid": "https://r2.ropensci.org/b576836f3fc9cf3a42fc810a57ff47799673f27236f7fd5f37695a169f993711",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38129802463"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-10-11T09:55:30.000Z",
      "commit": "62f26cb7ae4946b720e082819bfad3ac9ed73a3d",
      "fileid": "https://r2.ropensci.org/12691ff00ec39f9e5085e64adbb21ecd19e4c072a044889f28d242873db9c323",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38129802463"
    }
  ]
}