{ "_id": "6a1fe50eb401979e7343c02f", "Package": "wavClusteR", "Type": "Package", "Title": "Sensitive and highly resolved identification of RNA-protein\ninteraction sites in PAR-CLIP data", "Version": "2.47.0", "Date": "2015-05-07", "VignetteBuilder": "knitr", "Author": "Federico Comoglio and Cem Sievers", "Maintainer": "Federico Comoglio ", "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.r-universe.dev", "Date/Publication": "2026-04-28 12:39:13 UTC", "RemoteUrl": "https://github.com/bioc/wavClusteR", "RemoteRef": "HEAD", "RemoteSha": "231077608f4a1af7146a4b1c1f29e692fe93d5d8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 08:16:32 UTC", "User": "root" }, "MD5sum": "54b9a798c4265d1418d59ce78fd40037", "_user": "bioc", "_type": "src", "_file": "wavClusteR_2.47.0.tar.gz", "_fileid": "b2f1aeea68cb0de6875dc19499994ea5a507c5d78d64924b47346603026461d3", "_filesize": 767275, "_sha256": "b2f1aeea68cb0de6875dc19499994ea5a507c5d78d64924b47346603026461d3", "_created": "2026-06-03T08:16:32.000Z", "_published": "2026-06-03T08:25:49.980Z", "_jobs": [ { "job": 79251076319, "time": 267, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7379318943" }, { "job": 79251076292, "time": 492, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7379395464" }, { "job": 79251076386, "time": 494, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7379395630" }, { "job": 79251076275, "time": 344, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7379345465" }, { "job": 79251076344, "time": 385, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7379358757" }, { "job": 79250125836, "time": 355, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7379227652" }, { "job": 79251076577, "time": 232, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7379306737" }, { "job": 79251076301, "time": 445, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7379380105" }, { "job": 79251076320, "time": 411, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7379367880" }, { "job": 79251076370, "time": 408, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7379367364" } ], "_bioccheck": { "error": 2, "warning": 1, "note": 15 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26872194123", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/wavClusteR", "_commit": { "id": "231077608f4a1af7146a4b1c1f29e692fe93d5d8", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following 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": true, "_usedby": 0, "_updates": [ { "week": "2026-15", "n": 3 }, { "week": "2026-16", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_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": 431, "source": "https://www.bioconductor.org/packages/stats/bioc/wavClusteR" }, "_mentions": 4, "_searchresults": 11, "_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/HEAD/README.md", "_rundeps": [ "abind", "ade4", "AnnotationDbi", "askpass", "backports", "base64enc", "BH", "Biobase", "BiocBaseUtils", "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": 4.819543935541869, "_indexed": true, "_nocasepkg": "wavcluster", "_universes": [ "bioc", "federicocomoglio" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.47.0", "date": "2026-06-03T08:21:42.000Z", "distro": "noble", "commit": "231077608f4a1af7146a4b1c1f29e692fe93d5d8", "fileid": "a786cdb21f226b2db71a26eb1884b92cdd0386c42db04aeaf80a7b5757c190a5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26872194123" }, { "r": "4.6.0", "os": "linux", "version": "2.47.0", "date": "2026-06-03T08:21:38.000Z", "distro": "noble", "commit": "231077608f4a1af7146a4b1c1f29e692fe93d5d8", "fileid": "80f00268a4e1b1a73ccc00ab835d730bb537820a7e2084226db8528035a78a32", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26872194123" }, { "r": "4.5.3", "os": "mac", "version": "2.47.0", "date": "2026-06-03T08:19:27.000Z", "commit": "231077608f4a1af7146a4b1c1f29e692fe93d5d8", "fileid": "9fcb0b6f2353dc09694bc89690be2ec56ab280413d4a566c6a4f2269b0f02c19", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26872194123" }, { "r": "4.6.0", "os": "mac", "version": "2.47.0", "date": "2026-06-03T08:19:45.000Z", "commit": "231077608f4a1af7146a4b1c1f29e692fe93d5d8", "fileid": "1c20621dd1dd7ba42f37a7a18bccb4e6d08d83832016b70dc2f5f2b179334679", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26872194123" }, { "r": "4.6.0", "os": "wasm", "version": "2.47.0", "date": "2026-06-03T08:20:57.000Z", "commit": "231077608f4a1af7146a4b1c1f29e692fe93d5d8", "fileid": "fac8a319089255219edeeba4a97f2a6bfd0a790d3f6715759f6e5b5c5e8a43d5", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26872194123" }, { "r": "4.7.0", "os": "win", "version": "2.47.0", "date": "2026-06-03T08:20:24.000Z", "commit": "231077608f4a1af7146a4b1c1f29e692fe93d5d8", "fileid": "a4297d000582165fd3d5572604cddc76ddce66cc7df387cd5b10cf54f1077dcc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26872194123" }, { "r": "4.5.3", "os": "win", "version": "2.47.0", "date": "2026-06-03T08:20:08.000Z", "commit": "231077608f4a1af7146a4b1c1f29e692fe93d5d8", "fileid": "ce31df24bc19358002fa1d8adc6f8690b777a3745fa1537ed45f40f87e3791d4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26872194123" }, { "r": "4.6.0", "os": "win", "version": "2.47.0", "date": "2026-06-03T08:19:59.000Z", "commit": "231077608f4a1af7146a4b1c1f29e692fe93d5d8", "fileid": "ac29f37ac6acc2f8214a020b831f2c8df3e7e55acecadab9c972627298214856", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26872194123" } ] }