{
  "_id": "6a1b067c1d7bb097a0a03e3d",
  "Package": "wavClusteR",
  "Type": "Package",
  "Title": "Sensitive and highly resolved identification of RNA-protein\ninteraction sites in PAR-CLIP data",
  "Version": "2.46.0",
  "Date": "2015-05-07",
  "VignetteBuilder": "knitr",
  "Author": "Federico Comoglio and Cem Sievers",
  "Maintainer": "Federico Comoglio <federico.comoglio@gmail.com>",
  "Description": "The package provides an integrated pipeline for the\nanalysis of PAR-CLIP data. PAR-CLIP-induced transitions are\nfirst discriminated from sequencing errors, SNPs and additional\nnon-experimental sources by a non- parametric mixture model.\nThe protein binding sites (clusters) are then resolved at high\nresolution and cluster statistics are estimated using a\nrigorous Bayesian framework. Post-processing of the results,\ndata export for UCSC genome browser visualization and motif\nsearch analysis are provided. In addition, the package allows\nto integrate RNA-Seq data to estimate the False Discovery Rate\nof cluster detection. Key functions support parallel multicore\ncomputing. Note: while wavClusteR was designed for PAR-CLIP\ndata analysis, it can be applied to the analysis of other NGS\ndata obtained from experimental procedures that induce\nnucleotide substitutions (e.g. BisSeq).",
  "License": "GPL-2",
  "biocViews": "ImmunoOncology, Sequencing, Technology, RIPSeq, RNASeq,\nBayesian",
  "LazyLoad": "yes",
  "RoxygenNote": "7.0.2",
  "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev xz-utils\nzlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:39:13 UTC",
  "RemoteUrl": "https://github.com/bioc/wavClusteR",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "025643d8f3cb198b22fb72c2c4e054927c5598fe",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 10:54:49 UTC",
    "User": "root"
  },
  "MD5sum": "08fad0036d711597fff7730d26f2c5e0",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "wavClusteR_2.46.0.tar.gz",
  "_fileid": "ae79e8634fb4d22914c812b3d04162fa9945e8cf093c16618e6e4298b4acaf24",
  "_filesize": 767234,
  "_sha256": "ae79e8634fb4d22914c812b3d04162fa9945e8cf093c16618e6e4298b4acaf24",
  "_created": "2026-05-30T10:54:49.000Z",
  "_published": "2026-05-30T15:47:08.018Z",
  "_jobs": [
    {
      "job": 78644014580,
      "time": 278,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7307718519"
    },
    {
      "job": 78644014550,
      "time": 466,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307736030"
    },
    {
      "job": 78644014545,
      "time": 452,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307734712"
    },
    {
      "job": 78644014582,
      "time": 238,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7309358126"
    },
    {
      "job": 78644014576,
      "time": 317,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7309369185"
    },
    {
      "job": 78642742917,
      "time": 379,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307670987"
    },
    {
      "job": 78644014538,
      "time": 224,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307713301"
    },
    {
      "job": 78644014589,
      "time": 382,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307726986"
    },
    {
      "job": 78644014578,
      "time": 399,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307730145"
    },
    {
      "job": 78644014598,
      "time": 439,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307733887"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 1,
    "note": 15
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680568687",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/wavClusteR",
  "_commit": {
    "id": "025643d8f3cb198b22fb72c2c4e054927c5598fe",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777379953
  },
  "_maintainer": {
    "name": "Federico Comoglio",
    "email": "federico.comoglio@gmail.com",
    "login": "federicocomoglio",
    "linkedin": "in/fcomoglio",
    "orcid": "0000-0002-8970-6610",
    "description": "",
    "uuid": 5443822
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.2",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "version": ">= 1.31.8",
      "role": "Depends"
    },
    {
      "package": "Rsamtools",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "version": ">= 0.17.25",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "version": ">= 2.13.12",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "version": ">= 2.47.6",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "GenomicFeatures",
      "version": ">= 1.31.3",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "Hmisc",
      "role": "Imports"
    },
    {
      "package": "mclust",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
      "version": ">= 1.39.7",
      "role": "Imports"
    },
    {
      "package": "seqinr",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "txdbmaker",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Hsapiens.UCSC.hg19",
      "role": "Suggests"
    },
    {
      "package": "doMC",
      "role": "Enhances"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-15",
      "n": 3
    },
    {
      "week": "2026-16",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.47.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.46.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "sequencing",
    "technology",
    "ripseq",
    "rnaseq",
    "bayesian"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 442,
    "source": "https://www.bioconductor.org/packages/stats/bioc/wavClusteR"
  },
  "_mentions": 4,
  "_searchresults": 5,
  "_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/readme.html",
    "extra/readme.md",
    "extra/wavClusteR.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/federicocomoglio/wavcluster",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "annotateClusters",
    "estimateFDR",
    "exportClusters",
    "exportCoverage",
    "exportHighConfSub",
    "exportSequences",
    "filterClusters",
    "fitMixtureModel",
    "getAllSub",
    "getClusters",
    "getExpInterval",
    "getHighConfSub",
    "getMetaGene",
    "getMetaTSS",
    "plotSizeDistribution",
    "plotStatistics",
    "plotSubstitutions",
    "readSortedBam"
  ],
  "_datasets": [
    {
      "name": "model",
      "title": "Components of the non-parametric mixture moodel fitted on Ago2 PAR-CLIP data",
      "object": "model",
      "file": "model.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "wavClusteR-package",
      "title": "A comprehensive pipeline for the analysis of PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from sequencing errors, SNPs and additional non- experimental sources by a non-parametric mixture model. The protein binding sites (clusters) are then resolved at high resolution and cluster statistics are estimated using a rigorous Bayesian framework. Post-processing of the results, data export for UCSC genome browser visualization and motif search analysis are provided. In addition, the package allows to integrate RNA-Seq data to estimate the False Discovery Rate of cluster detection. Key functions support parallel multicore computing. Note: while wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other NGS data obtained from experimental procedures that induce nucleotide substitutions (e.g. BisSeq).",
      "topics": [
        "wavClusteR-package",
        "wavClusteR"
      ]
    },
    {
      "page": "annotateClusters",
      "title": "Annotate clusters with respect to transcript features",
      "topics": [
        "annotateClusters"
      ]
    },
    {
      "page": "estimateFDR",
      "title": "Estimate False Discovery Rate within the relative substitution frequency support by integrating PAR-CLIP data and RNA-Seq data",
      "topics": [
        "estimateFDR"
      ]
    },
    {
      "page": "exportClusters",
      "title": "Export clusters as BED track",
      "topics": [
        "exportClusters"
      ]
    },
    {
      "page": "exportCoverage",
      "title": "Export coverage as BigWig track",
      "topics": [
        "exportCoverage"
      ]
    },
    {
      "page": "exportHighConfSub",
      "title": "Export high-confidence substitutions as BED track",
      "topics": [
        "exportHighConfSub"
      ]
    },
    {
      "page": "exportSequences",
      "title": "Export cluster sequences for motif search analysis",
      "topics": [
        "exportSequences"
      ]
    },
    {
      "page": "filterClusters",
      "title": "Merge clusters and compute all relevant cluster statistics",
      "topics": [
        "filterClusters"
      ]
    },
    {
      "page": "FitMixtureModel",
      "title": "Fit a non-parametric mixture model from all identified substitutions",
      "topics": [
        "fitMixtureModel"
      ]
    },
    {
      "page": "getAllSub",
      "title": "Identify all substitutions observed across genomic positions exhibiting a specified minimum coverage",
      "topics": [
        "getAllSub"
      ]
    },
    {
      "page": "getClusters",
      "title": "Identify clusters containing high-confidence substitutions and resolve boundaries at high resolution",
      "topics": [
        "getClusters"
      ]
    },
    {
      "page": "getExpInterval",
      "title": "Identify the interval of relative substitution frequencies dominated by experimental induction.",
      "topics": [
        "getExpInterval"
      ]
    },
    {
      "page": "getHighConfSub",
      "title": "Classify substitutions based on identified RSF interval and return high confidence transitions",
      "topics": [
        "getHighConfSub"
      ]
    },
    {
      "page": "getMetaCoverage",
      "title": "Compute and plot distribution of average coverage or relative log-odds as metagene profile using identified clusters",
      "topics": [
        "getMetaCoverage"
      ]
    },
    {
      "page": "getMetaGene",
      "title": "Compute and plot metagene profile using identified clusters",
      "topics": [
        "getMetaGene"
      ]
    },
    {
      "page": "getMetaTSS",
      "title": "Compute and plot read densities in genomic regions around transcription start sites",
      "topics": [
        "getMetaTSS"
      ]
    },
    {
      "page": "model",
      "title": "Components of the non-parametric mixture moodel fitted on Ago2 PAR-CLIP data",
      "topics": [
        "model"
      ]
    },
    {
      "page": "plotSizeDistribution",
      "title": "Plot the distribution of cluster sizes",
      "topics": [
        "plotSizeDistribution"
      ]
    },
    {
      "page": "plotStatistics",
      "title": "Pairs plot visualization of clusters statistics",
      "topics": [
        "plotStatistics"
      ]
    },
    {
      "page": "plotSubstitutions",
      "title": "Barplot visualization of the number of genomic positions exhibiting a given substitution and, if model provided, additional diagnostic plots.",
      "topics": [
        "plotSubstitutions"
      ]
    },
    {
      "page": "readSortedBam",
      "title": "Load a sorted BAM file",
      "topics": [
        "readSortedBam"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/wavClusteR/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "ade4",
    "AnnotationDbi",
    "askpass",
    "backports",
    "base64enc",
    "BH",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "biomaRt",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "bslib",
    "cachem",
    "checkmate",
    "cigarillo",
    "cli",
    "cluster",
    "codetools",
    "colorspace",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "digest",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "foreach",
    "foreign",
    "formatR",
    "Formula",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "highr",
    "Hmisc",
    "hms",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "httr",
    "httr2",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mclust",
    "memoise",
    "mime",
    "nlme",
    "nnet",
    "openssl",
    "pillar",
    "pixmap",
    "pkgconfig",
    "png",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "rmarkdown",
    "rpart",
    "Rsamtools",
    "RSQLite",
    "rstudioapi",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "segmented",
    "Seqinfo",
    "seqinr",
    "snow",
    "sp",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "txdbmaker",
    "UCSC.utils",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "wavCluster_vignette.Rmd",
      "filename": "wavCluster_vignette.html",
      "title": "wavClusteR: a workflow for PAR-CLIP data analysis",
      "author": "Federico Comoglio and Cem Sievers",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2015-12-14 15:32:11",
      "modified": "2020-10-17 10:34:08",
      "commits": 12
    }
  ],
  "_score": 4.778151250383644,
  "_indexed": false,
  "_nocasepkg": "wavcluster",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/wavClusteR",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.46.0",
      "date": "2026-05-30T11:03:23.000Z",
      "distro": "noble",
      "commit": "025643d8f3cb198b22fb72c2c4e054927c5598fe",
      "fileid": "63110a0e1693edec4a57d13519eb2e3a4b08e1d1497f7a4f6906a2628fb43824",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680568687"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.46.0",
      "date": "2026-05-30T11:03:11.000Z",
      "distro": "noble",
      "commit": "025643d8f3cb198b22fb72c2c4e054927c5598fe",
      "fileid": "553ea5d7558cdcf3177d3bd877f41a3ef3b4ee827e1a6def3ba3bbe4b38068cb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680568687"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.46.0",
      "date": "2026-05-30T15:43:01.000Z",
      "commit": "025643d8f3cb198b22fb72c2c4e054927c5598fe",
      "fileid": "102ce580b19e6fa16fd0c251ee9a40ce65f89376d0c3fdc963ee02a55c8524e3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680568687"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.46.0",
      "date": "2026-05-30T15:44:10.000Z",
      "commit": "025643d8f3cb198b22fb72c2c4e054927c5598fe",
      "fileid": "372284d78352bef83430572e15cdeba422f4f6bcb81b1c0cabbd31191ef15b6e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680568687"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.46.0",
      "date": "2026-05-30T11:03:00.000Z",
      "commit": "025643d8f3cb198b22fb72c2c4e054927c5598fe",
      "fileid": "db8002cba38799e2dd2d0f60b3c2db386673035e299f25b1ec7e04cc77512b7f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680568687"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.46.0",
      "date": "2026-05-30T11:01:52.000Z",
      "commit": "025643d8f3cb198b22fb72c2c4e054927c5598fe",
      "fileid": "b63e6a05d0000b2a0fd7ed6ccd11de5cf18a6c3b1c92b4530cade7c7fbd0774d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680568687"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.46.0",
      "date": "2026-05-30T11:02:17.000Z",
      "commit": "025643d8f3cb198b22fb72c2c4e054927c5598fe",
      "fileid": "4604065bfb1a5f4eae6de000dd2bc7b469cbddcef084b29462a80072a3a7be7e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680568687"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.46.0",
      "date": "2026-05-30T11:02:51.000Z",
      "commit": "025643d8f3cb198b22fb72c2c4e054927c5598fe",
      "fileid": "77415f9cd4f3a99f402d70916d4ada622e3689efc5f6f908ab9f6603b2483215",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680568687"
    }
  ]
}