{ "_id": "6a1ad01b1d7bb097a09e123e", "Package": "GeneBreak", "Type": "Package", "Version": "1.43.0", "Title": "Gene Break Detection", "Author": "Evert van den Broek, Stef van Lieshout", "Maintainer": "Evert van den Broek ", "URL": "https://github.com/stefvanlieshout/GeneBreak", "Description": "Recurrent breakpoint gene detection on copy number\naberration profiles.", "License": "GPL-2", "biocViews": "aCGH, CopyNumberVariation, DNASeq, Genetics, Sequencing,\nWholeGenome, Visualization", "LazyData": "FALSE", "Config/pak/sysreqs": "libbz2-dev liblzma-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:42:03 UTC", "RemoteUrl": "https://github.com/bioc/GeneBreak", "RemoteRef": "HEAD", "RemoteSha": "09c10775dc2bfd4a523d43d6787e5976669f1f2d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:19:58 UTC", "User": "root" }, "MD5sum": "ec11950cb52fd253a01201d3e6eb6477", "_user": "bioc", "_type": "src", "_file": 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"name": "Evert van den Broek", "email": "vandenbroek.evert@gmail.com", "login": "evertbroek", "description": "", "uuid": 10812867 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.2", "role": "Depends" }, { "package": "QDNAseq", "role": "Depends" }, { "package": "CGHcall", "role": "Depends" }, { "package": "CGHbase", "role": "Depends" }, { "package": "GenomicRanges", "role": "Depends" }, { "package": "graphics", "role": "Imports" }, { "package": "methods", "role": "Imports" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.43.0", "bioc": "3.24" }, { "branch": "release", "version": "1.42.0", "bioc": "3.23" } ], "_topics": [ "acgh", "copynumbervariation", "dnaseq", "genetics", "sequencing", "wholegenome", "visualization" ], "_stars": 2, "_contributors": [ { "user": "stefvanlieshout", "count": 88, "uuid": 9608218 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 397, "source": "https://www.bioconductor.org/packages/stats/bioc/GeneBreak" }, "_mentions": 2, "_devurl": "https://github.com/stefvanlieshout/genebreak", "_searchresults": 6, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GeneBreak.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/stefvanlieshout/genebreak", "_realowner": "bioc", "_cranurl": false, "_exports": [ "accessOptions", "addGeneAnnotation", "bpFilter", "bpGenes", "bpPlot", "bpStats", "breakpointData", "breakpointsPerGene", "callData", "featureChromosomes", "featureInfo", "featuresPerGene", "geneChromosomes", "geneInfo", "getBreakpoints", "namesFeatures", "recurrentGenes", "sampleNames", "segmentData" ], "_datasets": [ { "name": "copynumber.data.chr18", "title": "CGHcall Example copynumber data hg18 chr18", "object": "copynumber.data.chr18", "file": "copynumber.data.chr18.rda", "class": [ "cghCall" ], "fields": [], "table": false, "tojson": false }, { "name": "copynumber.data.chr20", "title": "CGHcall Example copynumber data hg18 chr20", "object": "copynumber.data.chr20", "file": "copynumber.data.chr20.rda", "class": [ "cghCall" ], "fields": [], "table": false, "tojson": false }, { "name": "copynumber.data.chr21", "title": "CGHcall Example copynumber data hg18 chr21", "object": "copynumber.data.chr21", "file": "copynumber.data.chr21.rda", "class": [ "cghCall" ], "fields": [], "table": false, "tojson": false }, { "name": "ens.gene.ann.hg18", "title": "Gene Annotation hg18", "object": "ens.gene.ann.hg18", "file": "ens.gene.ann.hg18.rda", "class": [ "data.frame" ], "fields": [ "Gene", "EnsID", "Chromosome", "Start", "End", "band", "strand" ], "rows": 21604, "table": true, "tojson": true }, { "name": "ens.gene.ann.hg19", "title": "Gene Annotation hg19", "object": "ens.gene.ann.hg19", "file": "ens.gene.ann.hg19.rda", "class": [ "data.frame" ], "fields": [ "Gene", "EnsID", "Chromosome", "Start", "End", "band", "strand" ], "rows": 33625, "table": true, "tojson": true }, { "name": "ens.gene.ann.hg38", "title": "Gene Annotation hg38", "object": "ens.gene.ann.hg38", "file": "ens.gene.ann.hg38.rda", "class": [ "data.frame" ], "fields": [ "Gene", "EnsID", "Chromosome", "Start", "End", "band", "strand" ], "rows": 35141, "table": true, "tojson": true } ], "_help": [ { "page": "accessOptions-CopyNumberBreakPoints-method", "title": "Access Object Data. This method lists possible functions to access the data of the object.", "topics": [ "accessOptions", "accessOptions,CopyNumberBreakPoints-method" ] }, { "page": "addGeneAnnotation-CopyNumberBreakPoints-method", "title": "addGeneAnnotation", "topics": [ "addGeneAnnotation", "addGeneAnnotation,CopyNumberBreakPoints-method" ] }, { "page": "bpFilter-CopyNumberBreakPoints-method", "title": "bpFilter", "topics": [ "bpFilter", "bpFilter,CopyNumberBreakPoints-method" ] }, { "page": "bpGenes-CopyNumberBreakPointGenes-method", "title": "bpGenes", "topics": [ "bpGenes", "bpGenes,CopyNumberBreakPointGenes-method" ] }, { "page": "bpPlot-CopyNumberBreakPoints-method", "title": "bpPlot", "topics": [ "bpPlot", "bpPlot,CopyNumberBreakPoints-method" ] }, { "page": "bpStats-CopyNumberBreakPoints-method", "title": "bpStats", "topics": [ "bpStats", "bpStats,CopyNumberBreakPoints-method" ] }, { "page": "breakpointData-CopyNumberBreakPoints-method", "title": "Access Object breakpointData. This method returns a dataframe with breakpoint values per feature.", "topics": [ "breakpointData", "breakpointData,CopyNumberBreakPoints-method" ] }, { "page": "breakpointsPerGene-CopyNumberBreakPointGenes-method", "title": "Access Object breakpointsPerGene. This method returns a dataframe with breakpoints per gene.", "topics": [ "breakpointsPerGene", "breakpointsPerGene,CopyNumberBreakPointGenes-method" ] }, { "page": "callData-CopyNumberBreakPoints-method", "title": "Access Object callData. This method returns a dataframe with feature call values.", "topics": [ "callData", "callData,CopyNumberBreakPoints-method" ] }, { "page": "copynumber.data.chr18", "title": "CGHcall Example copynumber data hg18 chr18", "topics": [ "copynumber.data.chr18" ] }, { "page": "copynumber.data.chr20", "title": "CGHcall Example copynumber data hg18 chr20", "topics": [ "copynumber.data.chr20" ] }, { "page": "copynumber.data.chr21", "title": "CGHcall Example copynumber data hg18 chr21", "topics": [ "copynumber.data.chr21" ] }, { "page": "CopyNumberBreakPointGenes-class", "title": "An S4 class to represent a CopyNumberBreakPointGenes object", "topics": [ "CopyNumberBreakPointGenes", "CopyNumberBreakPointGenes-class" ] }, { "page": "CopyNumberBreakPoints-class", "title": "An S4 class to represent a CopyNumberBreakPoints object.", "topics": [ "CopyNumberBreakPoints", "CopyNumberBreakPoints-class" ] }, { "page": "ens.gene.ann.hg18", "title": "Gene Annotation hg18", "topics": [ "ens.gene.ann.hg18" ] }, { "page": "ens.gene.ann.hg19", "title": "Gene Annotation hg19", "topics": [ "ens.gene.ann.hg19" ] }, { "page": "ens.gene.ann.hg38", "title": "Gene Annotation hg38", "topics": [ "ens.gene.ann.hg38" ] }, { "page": "featureChromosomes-CopyNumberBreakPoints-method", "title": "Access Object featureChromosomes. This method returns a vector with feature chromosomes.", "topics": [ "featureChromosomes", "featureChromosomes,CopyNumberBreakPoints-method" ] }, { "page": "featureInfo-CopyNumberBreakPoints-method", "title": "Access Options featureInfo. This method returns a dataframe with feature annotations.", "topics": [ "featureInfo", "featureInfo,CopyNumberBreakPoints-method" ] }, { "page": "featuresPerGene-CopyNumberBreakPointGenes-method", "title": "Access Object featuresPerGene. This method returns a vector with gene-related features for a particular gene.", "topics": [ "featuresPerGene", "featuresPerGene,CopyNumberBreakPointGenes-method" ] }, { "page": "GeneBreak", "title": "GeneBreak: A package for gene breakpoint detection on copy number abberation data", "topics": [ "GeneBreak-package", "GeneBreak" ] }, { "page": "geneChromosomes-CopyNumberBreakPointGenes-method", "title": "Access Object geneChromosomes. This method returns a vector with gene chromosomes.", "topics": [ "geneChromosomes", "geneChromosomes,CopyNumberBreakPointGenes-method" ] }, { "page": "geneInfo-CopyNumberBreakPointGenes-method", "title": "Access Options geneInfo. This method returns a dataframe with gene annotations.", "topics": [ "geneInfo", "geneInfo,CopyNumberBreakPointGenes-method" ] }, { "page": "getBreakpoints", "title": "getBreakpoints", "topics": [ "getBreakpoints" ] }, { "page": "namesFeatures-CopyNumberBreakPoints-method", "title": "Access Object namesFeatures. This method returns a vector with feature names.", "topics": [ "namesFeatures", "namesFeatures,CopyNumberBreakPoints-method" ] }, { "page": "recurrentGenes-CopyNumberBreakPointGenes-method", "title": "Access Options recurrentGenes. This method returns a dataframe that contains genes that are recurrently affected across samples based on a FDR threshold.", "topics": [ "recurrentGenes", "recurrentGenes,CopyNumberBreakPointGenes-method" ] }, { "page": "sampleNames-CopyNumberBreakPoints-method", "title": "Access Object sampleNames. This method returns a vector with sample names.", "topics": [ "sampleNames", "sampleNames,CopyNumberBreakPoints-method" ] }, { "page": "segmentData-CopyNumberBreakPoints-method", "title": "Access Object segmentData. This method returns a dataframe with segment values.", "topics": [ "segmentData", "segmentData,CopyNumberBreakPoints-method" ] } ], "_readme": "https://github.com/bioc/GeneBreak/raw/HEAD/README.md", "_rundeps": [ "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bitops", "CGHbase", "CGHcall", "codetools", "cpp11", "crayon", "digest", "DNAcopy", "formatR", "futile.logger", "futile.options", "future", "future.apply", "generics", "GenomicRanges", "globals", "impute", "IRanges", "lambda.r", "limma", "listenv", "marray", "matrixStats", "parallelly", "QDNAseq", "R.methodsS3", "R.oo", "R.utils", "Rhtslib", "Rsamtools", "S4Vectors", "Seqinfo", "snow", "snowfall", "statmod", "XVector" ], "_vignettes": [ { "source": "GeneBreak.Rnw", "filename": "GeneBreak.pdf", "title": "GeneBreak", "engine": "utils::Sweave", "headings": [], "created": "2015-10-07 21:42:50", "modified": "2018-09-06 15:51:30", "commits": 2 } ], "_score": 4.6020599913279625, "_indexed": true, "_nocasepkg": "genebreak", "_universes": [ "bioc", "evertbroek", "stefvanlieshout" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.43.0", "date": "2026-05-30T08:23:22.000Z", "distro": "noble", "commit": "09c10775dc2bfd4a523d43d6787e5976669f1f2d", "fileid": "dee613c1d0a8370d2882e6d9cc20f5efa4528aafe2ef00aae6cc35d4edd44e96", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679009588" }, { "r": "4.6.0", "os": "linux", "version": "1.43.0", "date": "2026-05-30T08:23:43.000Z", "distro": "noble", "commit": "09c10775dc2bfd4a523d43d6787e5976669f1f2d", "fileid": "990b9fc0767e5fea4eb35778b665f1366aa0b3a602daaf5a43d966380985cd64", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679009588" }, { "r": "4.5.3", "os": "mac", "version": "1.43.0", "date": "2026-05-30T11:52:36.000Z", "commit": "09c10775dc2bfd4a523d43d6787e5976669f1f2d", "fileid": "dcb4eb7077b06a1efe82af3209bd30e8445f2e0d5d9a360c1590f9efb7ab401b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679009588" }, { "r": "4.6.0", "os": "mac", "version": "1.43.0", "date": "2026-05-30T11:53:11.000Z", "commit": "09c10775dc2bfd4a523d43d6787e5976669f1f2d", "fileid": "a3514e290808a360792992ae23ee639079f3c646d7e8b3b288cc1aad6a728d8a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679009588" }, { "r": "4.6.0", "os": "wasm", "version": "1.43.0", "date": "2026-05-30T08:22:31.000Z", "commit": "09c10775dc2bfd4a523d43d6787e5976669f1f2d", "fileid": "d98c3ab798e66e97aecb7d627036157d1dd2876cee7a1cdf76eccae7ccc75057", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679009588" }, { "r": "4.7.0", "os": "win", "version": "1.43.0", "date": "2026-05-30T08:21:49.000Z", "commit": "09c10775dc2bfd4a523d43d6787e5976669f1f2d", "fileid": "5157064810f1c8f989f823a2853c67743d95fe2046ebeb41b2e9e11b43ec2928", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679009588" }, { "r": "4.5.3", "os": "win", "version": "1.43.0", "date": "2026-05-30T08:21:39.000Z", "commit": "09c10775dc2bfd4a523d43d6787e5976669f1f2d", "fileid": "22a000642566640214403d68479f3a2a2ce779f4bce7e7a52da15c92dd4434c5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679009588" }, { "r": "4.6.0", "os": "win", "version": "1.43.0", "date": "2026-05-30T08:21:33.000Z", "commit": "09c10775dc2bfd4a523d43d6787e5976669f1f2d", "fileid": "56cde3340d5681b5dc9589e716855df4ac7873a546dee62141d4a66d37901395", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679009588" } ] }