{ "_id": "6a22718fcd65a98ecbd4924e", "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": "2026-06-05 06:44:28 UTC", "User": "root" }, "Author": "Maharani Ahsani Ummi [aut, cre],\nArief Gusnanto [aut]", "Maintainer": "Maharani Ahsani Ummi ", "MD5sum": "525c5943a9cddf5d1494bccdf366a1f5", "_user": "bioc", "_type": "src", "_file": "wavFeatExt_1.1.0.tar.gz", "_fileid": "045a48e1107c081c59d7afc13efc673195d35153fa57a88f822879345679d9fb", "_filesize": 457995, "_sha256": "045a48e1107c081c59d7afc13efc673195d35153fa57a88f822879345679d9fb", "_created": "2026-06-05T06:44:28.000Z", "_published": "2026-06-05T06:49:51.181Z", "_jobs": [ { "job": 79677965340, "time": 176, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7430508820" }, { "job": 79677965432, "time": 282, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7430533017" }, { "job": 79677965355, "time": 264, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7430528812" }, { "job": 79677965374, "time": 148, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7430501759" }, { "job": 79677965361, "time": 142, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7430500853" }, { "job": 79677418938, "time": 261, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7430465979" }, { "job": 79677965364, "time": 137, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7430499460" }, { "job": 79677965392, "time": 126, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7430497273" }, { "job": 79677965408, "time": 141, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7430500537" }, { "job": 79677965378, "time": 132, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7430498492" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 5 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26999779074", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/wavFeatExt", "_commit": { "id": "62f26cb7ae4946b720e082819bfad3ac9ed73a3d", "author": "A Wokaty ", "committer": "A Wokaty ", "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": "noble", "_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" }, { "branch": "release", "version": "1.0.0", "bioc": "3.23" } ], "_topics": [ "copynumbervariation", "genomicvariation", "featureextraction", "classification" ], "_stars": 0, "_contributors": [ { "user": "maharaniau", "count": 6, "uuid": 94630089 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 73, "source": "https://www.bioconductor.org/packages/stats/bioc/wavFeatExt" }, "_devurl": "https://github.com/maharaniau/wavfeatext", "_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/wavFeatExt.html", "manual.pdf" ], "_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": "2026-06-05T06:48:41.000Z", "distro": "noble", "commit": "62f26cb7ae4946b720e082819bfad3ac9ed73a3d", "fileid": "8a02557fad48a1deb096e2c455d4bfa37adac02b9e72247cf54d0ecdf6c896d8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26999779074" }, { "r": "4.6.0", "os": "linux", "version": "1.1.0", "date": "2026-06-05T06:48:35.000Z", "distro": "noble", "commit": "62f26cb7ae4946b720e082819bfad3ac9ed73a3d", "fileid": "d1a994e9f8368c949599d32e8b8524fa495f0d0cc47f6cbb22203eb7412e6d14", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26999779074" }, { "r": "4.5.3", "os": "mac", "version": "1.1.0", "date": "2026-06-05T06:46:32.000Z", "commit": "62f26cb7ae4946b720e082819bfad3ac9ed73a3d", "fileid": "e41ae3b1811ec4288c3517ad9cbaac6e140613a3a454194a3b2aefcedf81d6b5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26999779074" }, { "r": "4.6.0", "os": "mac", "version": "1.1.0", "date": "2026-06-05T06:46:27.000Z", "commit": "62f26cb7ae4946b720e082819bfad3ac9ed73a3d", "fileid": "8f592b815824288d071e4bb7161ad70602585cbb3d25b3423c3054d2fb0f317d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26999779074" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.0", "date": "2026-06-05T06:47:09.000Z", "commit": "62f26cb7ae4946b720e082819bfad3ac9ed73a3d", "fileid": "f6aa75ccb3bd3db6efcd16abed6bbc23795ffc7e754eeaaa0d26d09d597a50b4", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26999779074" }, { "r": "4.7.0", "os": "win", "version": "1.1.0", "date": "2026-06-05T06:45:56.000Z", "commit": "62f26cb7ae4946b720e082819bfad3ac9ed73a3d", "fileid": "d0c203e03584d75c824a0fb31856afad68799927db8d0411967847ae6280be95", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26999779074" }, { "r": "4.5.3", "os": "win", "version": "1.1.0", "date": "2026-06-05T06:46:07.000Z", "commit": "62f26cb7ae4946b720e082819bfad3ac9ed73a3d", "fileid": "ed90e119524f7cc625c263443dddfec7d8e72f283400ac727cbb99aebadff66f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26999779074" }, { "r": "4.6.0", "os": "win", "version": "1.1.0", "date": "2026-06-05T06:46:00.000Z", "commit": "62f26cb7ae4946b720e082819bfad3ac9ed73a3d", "fileid": "d429df91c24a70a226e2c6bfdd26b46e4cf3be27c6aacecc16e29c6e599e5bc0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26999779074" } ] }