{ "_id": "6a12c187acfb0bcc41d1deb7", "Package": "R453Plus1Toolbox", "Type": "Package", "Title": "A package for importing and analyzing data from Roche's Genome\nSequencer System", "Version": "1.63.0", "Date": "2026-04-05", "Author": "Hans-Ulrich Klein, Christoph Bartenhagen, Christian Ruckert", "Maintainer": "Hans-Ulrich Klein ", "Description": "The R453Plus1 Toolbox comprises useful functions for the\nanalysis of data generated by Roche's 454 sequencing platform.\nIt adds functions for quality assurance as well as for\nannotation and visualization of detected variants,\ncomplementing the software tools shipped by Roche with their\nproduct. Further, a pipeline for the detection of structural\nvariants is provided.", "License": "LGPL-3", "biocViews": "Sequencing, Infrastructure, DataImport, DataRepresentation,\nVisualization, QualityControl, ReportWriting", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:34:56 UTC", "RemoteUrl": "https://github.com/bioc/R453Plus1Toolbox", "RemoteRef": "HEAD", "RemoteSha": "8d8c63f53162b2fabd10980c3ac7e77f71e31e9e", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-04-30 15:29:03 UTC", "User": "root" }, "MD5sum": "3f91f3538da19d08e001d13766f45fd6", "_user": "bioc", "_type": "src", "_file": "R453Plus1Toolbox_1.63.0.tar.gz", "_fileid": "f8a8520d0c0bed145e3a3d6779d2602da2ee4c1a035de9d84facfdd6da0f6a70", "_filesize": 1206967, "_sha256": "f8a8520d0c0bed145e3a3d6779d2602da2ee4c1a035de9d84facfdd6da0f6a70", "_created": "2026-04-30T15:29:03.000Z", "_jobs": [ { "job": 77586039273, "time": 462, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "6734164736" }, { "job": 77586039369, "time": 588, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "6734112618" }, { "job": 77586039267, "time": 765, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "6734276819" }, { "job": 77586039461, "time": 513, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "6734083531" }, { "job": 77586039394, "time": 639, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "6734231026" }, { "job": 77586039424, "time": 408, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "6736055749" }, { "job": 77586039387, "time": 936, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "6735076201" }, { "job": 77586039373, "time": 465, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "6736072016" }, { "job": 77586039285, "time": 1021, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "6735100574" }, { "job": 77586039237, "time": 1056, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6733892212" }, { "job": 77586039128, "time": 238, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 77586039291, "time": 594, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "6734210861" }, { "job": 77586039393, "time": 606, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "6734225759" }, { "job": 77586039304, "time": 579, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "6734205140" } ], "_bioccheck": { "error": 3, "warning": 3, "note": 19 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25173438673", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/R453Plus1Toolbox", "_commit": { "id": "8d8c63f53162b2fabd10980c3ac7e77f71e31e9e", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379696 }, "_maintainer": { "name": "Hans-Ulrich Klein", "email": "h.klein@uni-muenster.de" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.12.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "VariantAnnotation", "version": ">= 1.25.11", "role": "Depends" }, { "package": "Biostrings", "version": ">= 2.47.6", "role": "Depends" }, { "package": "pwalign", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "utils", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "xtable", "role": "Imports" }, { "package": "R2HTML", "role": "Imports" }, { "package": "TeachingDemos", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "S4Vectors", "version": ">= 0.17.25", "role": "Imports" }, { "package": "IRanges", "version": ">= 2.13.12", "role": "Imports" }, { "package": "XVector", "role": "Imports" }, { "package": "GenomicRanges", "version": ">= 1.31.8", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "biomaRt", "role": "Imports" }, { "package": "BSgenome", "version": ">= 1.47.3", "role": "Imports" }, { "package": "Rsamtools", "role": "Imports" }, { "package": "ShortRead", "version": ">= 1.37.1", "role": "Imports" }, { "package": "rtracklayer", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg19", "role": "Suggests" }, { "package": "BSgenome.Scerevisiae.UCSC.sacCer2", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-14", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.63.0", "bioc": "3.24" }, { "branch": "release", "version": "1.62.0", "bioc": "3.23" } ], "_topics": [ "sequencing", "infrastructure", "dataimport", "datarepresentation", "visualization", "qualitycontrol", "reportwriting" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 410, "source": "https://www.bioconductor.org/packages/stats/bioc/R453Plus1Toolbox" }, "_mentions": 1, "_searchresults": 10, "_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/R453Plus1Toolbox.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "addRead", "alignedReadsC1", "alignedReadsC1<-", "alignedReadsC2", "alignedReadsC2<-", "alignShortReads", "annotatedVariants", "annotateVariants", "assayDataAmp", "assayDataAmp<-", "ava2vcf", "AVASet", "baseFrequency", "baseQualityHist", "baseQualityStats", "calculateTiTv", "clipAdapterLeft", "clipAdapterLeft<-", "clipAdapterRight", "clipAdapterRight<-", "clipQualityLeft", "clipQualityLeft<-", "clipQualityRight", "clipQualityRight<-", "commonAlignC1", "commonAlignC1<-", "commonAlignC2", "commonAlignC2<-", "commonBpsC1", "commonBpsC1<-", "commonBpsC2", "commonBpsC2<-", "complexity.dust", "complexity.entropy", "coverageOnTarget", "demultiplexReads", "detectBreakpoints", "dinucleotideOddsRatio", "extendedCIGARToList", "fDataAmp", "featureDataAmp", "featureDataAmp<-", "filterChimericReads", "flowChars", "flowChars<-", "flowgram", "flowgram<-", "flowgramBarplot", "flowgramFormat", "flowgramFormat<-", "flowgrams", "flowgrams<-", "flowIndexes", "flowIndexes<-", "gcContent", "gcContentHist", "gcPerPosition", "genomeSequencerMIDs", "getAlignedReads", "getRead", "getReadStatus", "getVariantPercentages", "homopolymerHist", "htmlReport", "keySequence", "keySequence<-", "listToExtendedCIGAR", "MapperSet", "mergeBreakpoints", "name", "name<-", "nucleotideCharts", "plotAmpliconCoverage", "plotChimericReads", "plotVariants", "plotVariationFrequency", "positionQualityBoxplot", "quality", "quality<-", "qualityReportSFF", "read", "read<-", "readLengthHist", "readLengthStats", "reads", "reads<-", "readSFF", "readsOnTarget", "referenceSequences", "referenceSequences<-", "removeLinker", "seqsC1", "seqsC1<-", "seqsC2", "seqsC2<-", "sequenceCaptureLinkers", "sequenceQualityHist", "setVariantFilter", "sff2fastq", "writeSFF" ], "_datasets": [ { "name": "avaSetExample", "title": "Amplicon Variant Analyzer data import", "object": "avaSetExample", "file": "avaSetExample.RData", "class": [ "AVASet" ], "fields": [], "table": false, "tojson": false }, { "name": "avaSetFiltered", "title": "Amplicon Variant Analyzer data import", "object": "avaSetFiltered", "file": "avaSetFiltered.RData", "class": [ "AVASet" ], "fields": [], "table": false, "tojson": false }, { "name": "avaSetFiltered_annot", "title": "AVASet variant annotations", "object": "avaSetFiltered_annot", "file": "avaSetFiltered_annot.RData", "class": [ "AnnotatedVariants" ], "fields": [], "table": false, "tojson": false }, { "name": "breakpoints", "title": "Putative breakpoints of chimeric reads", "object": "breakpoints", "file": "breakpoints.RData", "class": [ "Breakpoints" ], "fields": [], "table": false, "tojson": false }, { "name": "captureArray", "title": "Custom capture array design", "object": "captureArray", "file": "captureArray.RData", "class": [ "CompressedIRangesList" ], "fields": [], "table": false, "tojson": false }, { "name": "mapperSetExample", "title": "GS Reference Mapper data import", "object": "mapperSetExample", "file": "mapperSetExample.RData", "class": [ "MapperSet" ], "fields": [], "table": false, "tojson": false }, { "name": "mutationInfo", "title": "Example data for 'plotVariants'", "object": "plotVariantsExample", "file": "plotVariantsExample.RData", "class": [ "data.frame" ], "fields": [ "mutation", "legend", "color" ], "rows": 4, "table": true, "tojson": true }, { "name": "regions", "title": "Example data for 'plotVariants'", "object": "plotVariantsExample", "file": "plotVariantsExample.RData", "class": [ "data.frame" ], "fields": [ "name", "start", "end", "color" ], "rows": 2, "table": true, "tojson": true }, { "name": "variants", "title": "Example data for 'plotVariants'", "object": "plotVariantsExample", "file": "plotVariantsExample.RData", "class": [ "data.frame" ], "fields": [ "label", "pos", "mutation", "color" ], "rows": 4, "table": true, "tojson": true } ], "_help": [ { "page": "alignShortReads", "title": "Exact alignment of DNA sequences against a reference", "topics": [ "alignShortReads", "alignShortReads,AVASet,BSgenome,character,logical-method", "alignShortReads,AVASet,BSgenome,character,missing-method", "alignShortReads,AVASet,BSgenome,missing,logical-method", "alignShortReads,AVASet,BSgenome,missing,missing-method", "alignShortReads,DNAStringSet,BSgenome,character,logical-method", "alignShortReads,DNAStringSet,BSgenome,character,missing-method", "alignShortReads,DNAStringSet,BSgenome,missing,logical-method", "alignShortReads,DNAStringSet,BSgenome,missing,missing-method" ] }, { "page": "AnnotatedVariants-class", "title": "Class \"AnnotatedVariants\"", "topics": [ "annotatedVariants", "annotatedVariants,AnnotatedVariants-method", "AnnotatedVariants-class", "annotatedVariants<-,AnnotatedVariants,list-method", "names,AnnotatedVariants-method", "names<-,AnnotatedVariants,character-method" ] }, { "page": "annotateVariants", "title": "Adds genomic information to variants", "topics": [ "annotateVariants", "annotateVariants,AVASet,missing-method", "annotateVariants,data.frame,missing-method", "annotateVariants,MapperSet,BSgenome-method", "annotateVariants,MapperSet,missing-method" ] }, { "page": "assayDataAmp", "title": "Access the amplicon data of an AVASet.", "topics": [ "assayDataAmp" ] }, { "page": "ava2vcf", "title": "Convert an AVASet object into a VCF object", "topics": [ "ava2vcf", "ava2vcf,AVASet-method" ] }, { "page": "AVASet", "title": "Creating an AVASet", "topics": [ "AVASet", "AVASet,character,character,missing,missing,missing,missing,missing-method", "AVASet,character,missing,character,character,character,character,character-method", "AVASet,character,missing,character,character,character,missing,missing-method", "AVASet,character,missing,missing,missing,missing,missing,missing-method" ] }, { "page": "AVASet-class", "title": "Class to contain Amplicon Variant Analyzer Output", "topics": [ "alignShortReads,AVASet,DNAStringSet,character-method", "annotateVariants,AVASet-method", "assayDataAmp,AVASet-method", "assayDataAmp<-", "assayDataAmp<-,AVASet,AssayData-method", "AVASet-class", "fDataAmp,AVASet-method", "featureDataAmp,AVASet-method", "featureDataAmp<-", "featureDataAmp<-,AVASet,AnnotatedDataFrame-method", "getVariantPercentages,AVASet-method", "htmlReport,AVASet-method", "referenceSequences,AVASet-method", "referenceSequences<-", "referenceSequences<-,AVASet,AlignedRead-method", "setVariantFilter,AVASet-method", "[,AVASet,ANY,ANY,ANY-method", "[,AVASet,ANY,ANY-method" ] }, { "page": "avaSetExample", "title": "Amplicon Variant Analyzer data import", "topics": [ "avaSetExample" ] }, { "page": "avaSetFiltered", "title": "Amplicon Variant Analyzer data import", "topics": [ "avaSetFiltered" ] }, { "page": "avaSetFiltered_annot", "title": "AVASet variant annotations", "topics": [ "avaSetFiltered_annot" ] }, { "page": "baseFrequency", "title": "Absolute And Relative Frequency Of The Four Bases.", "topics": [ "baseFrequency", "baseFrequency,DNAStringSet-method", "baseFrequency,SFFContainer-method", "baseFrequency,ShortRead-method" ] }, { "page": "baseQualityHist", "title": "Plot A Histogram Of The Base Qualities.", "topics": [ "baseQualityHist", "baseQualityHist,QualityScaledDNAStringSet-method", "baseQualityHist,SFFContainer-method", "baseQualityHist,ShortReadQ-method" ] }, { "page": "baseQualityStats", "title": "Statistics Of Base Quality", "topics": [ "baseQualityStats", "baseQualityStats,QualityScaledDNAStringSet-method", "baseQualityStats,SFFContainer-method", "baseQualityStats,ShortReadQ-method" ] }, { "page": "breakpoints", "title": "Putative breakpoints of chimeric reads", "topics": [ "breakpoints" ] }, { "page": "Breakpoints-class", "title": "Class \"Breakpoints\"", "topics": [ "alignedReadsC1", "alignedReadsC1,Breakpoints-method", "alignedReadsC1<-", "alignedReadsC1<-,Breakpoints,list-method", "alignedReadsC2", "alignedReadsC2,Breakpoints-method", "alignedReadsC2<-", "alignedReadsC2<-,Breakpoints,list-method", "Breakpoints-class", "commonAlignC1", "commonAlignC1,Breakpoints-method", "commonAlignC1<-", "commonAlignC1<-,Breakpoints,list-method", "commonAlignC2", "commonAlignC2,Breakpoints-method", "commonAlignC2<-", "commonAlignC2<-,Breakpoints,list-method", "commonBpsC1", "commonBpsC1,Breakpoints-method", "commonBpsC1<-", "commonBpsC1<-,Breakpoints,list-method", "commonBpsC2", "commonBpsC2,Breakpoints-method", "commonBpsC2<-", "commonBpsC2<-,Breakpoints,list-method", "length,Breakpoints-method", "mergeBreakpoints,Breakpoints,missing,list-method", "mergeBreakpoints,Breakpoints,missing,missing-method", "mergeBreakpoints,Breakpoints,numeric,missing-method", "names,Breakpoints-method", "names<-,Breakpoints,ANY-method", "plotChimericReads,Breakpoints-method", "seqsC1", "seqsC1,Breakpoints-method", "seqsC1<-", "seqsC1<-,Breakpoints,list-method", "seqsC2", "seqsC2,Breakpoints-method", "seqsC2<-", "seqsC2<-,Breakpoints,list-method", "[,Breakpoints,ANY,ANY,ANY-method", "[,Breakpoints,ANY,ANY-method" ] }, { "page": "calculateTiTv", "title": "Calculate transition transversion ratio", "topics": [ "calculateTiTv", "calculateTiTv,AVASet-method", "calculateTiTv,MapperSet-method" ] }, { "page": "captureArray", "title": "Custom capture array design", "topics": [ "captureArray" ] }, { "page": "complexity.dust", "title": "Sequence Complexity Using The DUST Algorithm", "topics": [ "complexity.dust", "complexity.dust,DNAStringSet-method", "complexity.dust,SFFContainer-method", "complexity.dust,ShortRead-method" ] }, { "page": "complexity.entropy", "title": "Sequence Complexity Using The Shannon-Wiener Algorithm", "topics": [ "complexity.entropy", "complexity.entropy,DNAStringSet-method", "complexity.entropy,SFFContainer-method", "complexity.entropy,ShortRead-method" ] }, { "page": "convertCigar", "title": "Basic functions for CIGAR strings", "topics": [ "convertCigar", "extendedCIGARToList", "listToExtendedCIGAR" ] }, { "page": "coverageOnTarget", "title": "Computes the coverage restricted to the target region.", "topics": [ "coverageOnTarget", "coverageOnTarget,list,GRanges-method" ] }, { "page": "demultiplexReads", "title": "Performs MID/Multiplex filtering", "topics": [ "demultiplexReads", "demultiplexReads,XStringSet,XStringSet,missing,logical-method", "demultiplexReads,XStringSet,XStringSet,missing,missing-method", "demultiplexReads,XStringSet,XStringSet,numeric,logical-method", "demultiplexReads,XStringSet,XStringSet,numeric,missing-method" ] }, { "page": "detectBreakpoints", "title": "Clustering and consensus breakpoint detection for chimeric reads", "topics": [ "detectBreakpoints", "detectBreakpoints,list-method" ] }, { "page": "dinucleotideOddsRatio", "title": "Dinucleotide Odds Ratio", "topics": [ "dinucleotideOddsRatio", "dinucleotideOddsRatio,DNAStringSet-method", "dinucleotideOddsRatio,SFFContainer-method", "dinucleotideOddsRatio,ShortRead-method" ] }, { "page": "fDataAmp", "title": "Access the amplicon data of an AVASet.", "topics": [ "fDataAmp" ] }, { "page": "featureDataAmp", "title": "Access the amplicon data of an AVASet", "topics": [ "featureDataAmp" ] }, { "page": "filterChimericReads", "title": "Extract chimeric reads and apply filtering steps to remove artificial chimeric reads.", "topics": [ "filterChimericReads", "filterChimericReads,list,IntegerRangesList,DNAString,missing,missing-method", "filterChimericReads,list,IntegerRangesList,DNAString,numeric,numeric-method", "filterChimericReads,list,IntegerRangesList,missing,missing,missing-method", "filterChimericReads,list,IntegerRangesList,missing,numeric,numeric-method", "filterChimericReads,list,missing,DNAString,missing,missing-method", "filterChimericReads,list,missing,DNAString,numeric,numeric-method", "filterChimericReads,list,missing,missing,missing,missing-method", "filterChimericReads,list,missing,missing,numeric,numeric-method" ] }, { "page": "flowgramBarplot", "title": "Create A Barplot Of The Flow Intensities", "topics": [ "flowgramBarplot", "flowgramBarplot,SFFRead-method" ] }, { "page": "gcContent", "title": "Calculate The Overall GC-Content", "topics": [ "gcContent", "gcContent,DNAStringSet-method", "gcContent,SFFContainer-method", "gcContent,ShortRead-method" ] }, { "page": "gcContentHist", "title": "GC-Content Histogram", "topics": [ "gcContentHist", "gcContentHist,DNAStringSet-method", "gcContentHist,SFFContainer-method", "gcContentHist,ShortRead-method" ] }, { "page": "gcPerPosition", "title": "GC-Content Per Position", "topics": [ "gcPerPosition", "gcPerPosition,DNAStringSet-method", "gcPerPosition,SFFContainer-method", "gcPerPosition,ShortRead-method" ] }, { "page": "genomeSequencerMIDs", "title": "Retrieve GS multiplex sequences", "topics": [ "genomeSequencerMIDs", "genomeSequencerMIDs,character-method", "genomeSequencerMIDs,missing-method" ] }, { "page": "getAlignedReads", "title": "Import reads from an Amplicon Variant Analyzer project", "topics": [ "getAlignedReads", "getAlignedReads,AVASet-method" ] }, { "page": "getAminoAbbr", "title": "Get amino acid abbreviations", "topics": [ "getAminoAbbr" ] }, { "page": "getVariantPercentages", "title": "Variant coverage", "topics": [ "getVariantPercentages" ] }, { "page": "homopolymerHist", "title": "Create A Histogram Of The Homopolymer Stretches", "topics": [ "homopolymerHist", "homopolymerHist,SFFRead-method" ] }, { "page": "htmlReport", "title": "HTML-Report Builder for the AVASet and MapperSet", "topics": [ "htmlReport" ] }, { "page": "MapperSet", "title": "Creating a MapperSet", "topics": [ "MapperSet", "MapperSet,character-method" ] }, { "page": "MapperSet-class", "title": "Class to Contain GS Reference Mapper Output", "topics": [ "annotateVariants,MapperSet-method", "getReadStatus", "getReadStatus,MapperSet-method", "getVariantPercentages,MapperSet-method", "htmlReport,MapperSet-method", "MapperSet-class", "setVariantFilter,MapperSet-method" ] }, { "page": "mapperSetExample", "title": "GS Reference Mapper data import", "topics": [ "mapperSetExample" ] }, { "page": "mergeBreakpoints", "title": "Identify and merge related breakpoints caused by the same variant.", "topics": [ "mergeBreakpoints" ] }, { "page": "mutationInfo", "title": "Example data for 'plotVariants'", "topics": [ "mutationInfo" ] }, { "page": "nucleotideCharts", "title": "Nucleotide Charts", "topics": [ "nucleotideCharts", "nucleotideCharts,DNAStringSet-method", "nucleotideCharts,SFFContainer-method", "nucleotideCharts,ShortRead-method" ] }, { "page": "plotAmpliconCoverage", "title": "Creates a plot visualizing the number of reads per amplicon", "topics": [ "plotAmpliconCoverage", "plotAmpliconCoverage,AVASet,character,logical-method", "plotAmpliconCoverage,AVASet,character,missing-method", "plotAmpliconCoverage,AVASet,missing,logical-method", "plotAmpliconCoverage,AVASet,missing,missing-method" ] }, { "page": "plotChimericReads", "title": "Plots chimeric reads", "topics": [ "plotChimericReads" ] }, { "page": "plotVariants", "title": "Plots variant positions", "topics": [ "plotVariants", "plotVariants,AnnotatedVariants,character-method", "plotVariants,data.frame,character-method" ] }, { "page": "plotVariationFrequency", "title": "Create an AVA style variation frequency plot", "topics": [ "plotVariationFrequency", "plotVariationFrequency,character,numeric-method" ] }, { "page": "positionQualityBoxplot", "title": "Boxplot Of The Quality For Each Position", "topics": [ "positionQualityBoxplot", "positionQualityBoxplot,QualityScaledDNAStringSet-method", "positionQualityBoxplot,SFFContainer-method", "positionQualityBoxplot,ShortReadQ-method" ] }, { "page": "qualityReportSFF", "title": "Function To Create A Quality Report In PDF Format", "topics": [ "qualityReportSFF" ] }, { "page": "readLengthHist", "title": "Histogram Of The Read Lengths", "topics": [ "readLengthHist", "readLengthHist,DNAStringSet-method", "readLengthHist,SFFContainer-method", "readLengthHist,ShortRead-method" ] }, { "page": "readLengthStats", "title": "Statistics For The Read Lengths", "topics": [ "readLengthStats", "readLengthStats,DNAStringSet-method", "readLengthStats,SFFContainer-method", "readLengthStats,ShortRead-method" ] }, { "page": "readSFF", "title": "Function To Read In Roche's .sff Files", "topics": [ "readSFF" ] }, { "page": "readsOnTarget", "title": "Check for each read whether it aligns within the given region.", "topics": [ "readsOnTarget", "readsOnTarget,list,GRanges-method" ] }, { "page": "referenceSequences", "title": "Access the reference sequences of an AVASet", "topics": [ "referenceSequences" ] }, { "page": "regions", "title": "Example data for 'plotVariants'", "topics": [ "regions" ] }, { "page": "removeLinker", "title": "Remove linker sequences located at the start of short reads", "topics": [ "removeLinker", "removeLinker,XStringSet,DNAString,logical,numeric,numeric-method", "removeLinker,XStringSet,DNAString,missing,missing,missing-method" ] }, { "page": "sequenceCaptureLinkers", "title": "Retrieve NimbleGen's sequence capture linkers", "topics": [ "sequenceCaptureLinkers", "sequenceCaptureLinkers,character-method", "sequenceCaptureLinkers,missing-method" ] }, { "page": "sequenceQualityHist", "title": "A Histogram Of The Sequence Qualities", "topics": [ "sequenceQualityHist", "sequenceQualityHist,QualityScaledDNAStringSet-method", "sequenceQualityHist,SFFContainer-method", "sequenceQualityHist,ShortReadQ-method" ] }, { "page": "setVariantFilter", "title": "Filters output of variant information", "topics": [ "setVariantFilter" ] }, { "page": "sff2fastq", "title": "Write A SFFContainer Object To A FASTQ File", "topics": [ "sff2fastq", "sff2fastq,SFFContainer-method" ] }, { "page": "SFFContainer-class", "title": "Class '\"SFFContainer\"'", "topics": [ "addRead", "addRead,SFFContainer,SFFRead-method", "clipAdapterLeft", "clipAdapterLeft,SFFContainer-method", "clipAdapterLeft<-", "clipAdapterLeft<-,SFFContainer,numeric-method", "clipAdapterRight", "clipAdapterRight,SFFContainer-method", "clipAdapterRight<-", "clipAdapterRight<-,SFFContainer,numeric-method", "clipQualityLeft", "clipQualityLeft,SFFContainer-method", "clipQualityLeft<-", "clipQualityLeft<-,SFFContainer,numeric-method", "clipQualityRight", "clipQualityRight,SFFContainer-method", "clipQualityRight<-", "clipQualityRight<-,SFFContainer,numeric-method", "flowChars", "flowChars,SFFContainer-method", "flowChars<-", "flowChars<-,SFFContainer,character-method", "flowgramFormat", "flowgramFormat,SFFContainer-method", "flowgramFormat<-", "flowgramFormat<-,SFFContainer,numeric-method", "flowgrams", "flowgrams,SFFContainer-method", "flowgrams<-", "flowgrams<-,SFFContainer,list-method", "flowIndexes", "flowIndexes,SFFContainer-method", "flowIndexes<-", "flowIndexes<-,SFFContainer,list-method", "getRead", "getRead,SFFContainer,character-method", "keySequence", "keySequence,SFFContainer-method", "keySequence<-", "keySequence<-,SFFContainer,character-method", "name", "name,SFFContainer-method", "name<-", "name<-,SFFContainer,character-method", "reads", "reads,SFFContainer-method", "reads<-", "reads<-,SFFContainer,QualityScaledDNAStringSet-method", "SFFContainer", "SFFContainer-class", "[,SFFContainer,ANY,ANY,ANY-method", "[,SFFContainer,ANY,ANY-method" ] }, { "page": "SFFRead-class", "title": "Class '\"SFFRead\"'", "topics": [ "clipAdapterLeft,SFFRead-method", "clipAdapterLeft<-,SFFRead,numeric-method", "clipAdapterRight,SFFRead-method", "clipAdapterRight<-,SFFRead,numeric-method", "clipQualityLeft,SFFRead-method", "clipQualityLeft<-,SFFRead,numeric-method", "clipQualityRight,SFFRead-method", "clipQualityRight<-,SFFRead,numeric-method", "flowChars,SFFRead-method", "flowChars<-,SFFRead,character-method", "flowgram", "flowgram,SFFRead-method", "flowgram<-", "flowgram<-,SFFRead,numeric-method", "flowgramFormat,SFFRead-method", "flowgramFormat<-,SFFRead,numeric-method", "flowIndexes,SFFRead-method", "flowIndexes<-,SFFRead,numeric-method", "keySequence,SFFRead-method", "keySequence<-,SFFRead,character-method", "name,SFFRead-method", "name<-,SFFRead,character-method", "quality,SFFRead-method", "quality<-", "quality<-,SFFRead,BString-method", "read", "read,SFFRead-method", "read<-", "read<-,SFFRead,QualityScaledDNAStringSet-method", "SFFRead", "SFFRead-class" ] }, { "page": "variants", "title": "Example data for 'plotVariants'", "topics": [ "variants" ] }, { "page": "writeSFF", "title": "Function To Write Files In Roche's .sff Format", "topics": [ "writeSFF" ] } ], "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "BSgenome", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "dbplyr", "DelayedArray", "deldir", "dplyr", "fastmap", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "glue", "hms", "httr", "httr2", "hwriter", "interp", "IRanges", "jpeg", "jsonlite", "KEGGREST", "lambda.r", "lattice", "latticeExtra", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pillar", "pkgconfig", "png", "prettyunits", "progress", "purrr", "pwalign", "R2HTML", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppEigen", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "ShortRead", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "TeachingDemos", "tibble", "tidyr", "tidyselect", "utf8", "VariantAnnotation", "vctrs", "withr", "XML", "xml2", "xtable", "XVector", "yaml" ], "_vignettes": [ { "source": "vignette.Rnw", "filename": "vignette.pdf", "title": "A package for importing and analyzing data from Roche's Genome Sequencer System", "engine": "utils::Sweave", "headings": [], "created": "2013-10-13 16:28:23", "modified": "2026-04-05 16:01:06", "commits": 4 } ], "_score": 3.4771212547196626, "_indexed": true, "_nocasepkg": "r453plus1toolbox", "_universes": [ "bioc" ], "_failure": { "version": "1.63.0", "commit": { "id": "8d8c63f53162b2fabd10980c3ac7e77f71e31e9e", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379696 }, "buildurl": "https://github.com/r-universe/bioc/actions/runs/26658028437", "date": "2026-06-01T06:35:20.448Z", "job": { "job": 78798310844, "time": 292, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7324828929" } }, "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.63.0", "date": "2026-04-30T15:38:09.000Z", "distro": "noble", "arch": "aarch64", "commit": "8d8c63f53162b2fabd10980c3ac7e77f71e31e9e", "fileid": "1a227243ff50fb4957f7376243e2419601f908cc050e43054ca7f29f96040cdf", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173438673" }, { "r": "4.7.0", "os": "linux", "version": "1.63.0", "date": "2026-04-30T15:44:27.000Z", "distro": "noble", "arch": "x86_64", "commit": "8d8c63f53162b2fabd10980c3ac7e77f71e31e9e", "fileid": "e35dec9287804f7ad6f5ca0c7c100c85a375e52cb5dd0ded72c44215e4a74c69", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173438673" }, { "r": "4.6.0", "os": "linux", "version": "1.63.0", "date": "2026-04-30T15:36:50.000Z", "distro": "noble", "arch": "aarch64", "commit": "8d8c63f53162b2fabd10980c3ac7e77f71e31e9e", "fileid": "e7b869d1c28005945cf1cf1d3b1aaec488a7a8802140b0335bfd256427977bd1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173438673" }, { "r": "4.6.0", "os": "linux", "version": "1.63.0", "date": "2026-04-30T15:43:11.000Z", "distro": "noble", "arch": "x86_64", "commit": "8d8c63f53162b2fabd10980c3ac7e77f71e31e9e", "fileid": "cf5584c082d1178d44e7e566886703946b1706c8639408fe19762e6461716a32", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173438673" }, { "r": "4.5.3", "os": "mac", "version": "1.63.0", "date": "2026-04-30T17:14:28.000Z", "arch": "aarch64", "commit": "8d8c63f53162b2fabd10980c3ac7e77f71e31e9e", "fileid": "f194a7082af3effa51b997cfd491f255e0db03f0150cce286c4f8d539c06f23c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173438673" }, { "r": "4.5.3", "os": "mac", "version": "1.63.0", "date": "2026-04-30T16:20:20.000Z", "arch": "x86_64", "commit": "8d8c63f53162b2fabd10980c3ac7e77f71e31e9e", "fileid": "2c6f55a02a75c8d2d4b5430be8d4569c16386ac86b824c5598c4233fa69fbe99", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173438673" }, { "r": "4.6.0", "os": "mac", "version": "1.63.0", "date": "2026-04-30T17:14:04.000Z", "arch": "aarch64", "commit": "8d8c63f53162b2fabd10980c3ac7e77f71e31e9e", "fileid": "7eda08aac179e8e0e6ce54c4e39ccd4dede7fabda57b465b5d43b2aa30f18aec", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173438673" }, { "r": "4.6.0", "os": "mac", "version": "1.63.0", "date": "2026-04-30T16:21:51.000Z", "arch": "x86_64", "commit": "8d8c63f53162b2fabd10980c3ac7e77f71e31e9e", "fileid": "20cf7c776e0b48556dacc84b8aecfe7a413a2b127751f8a596e2f50352ce6ba9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173438673" }, { "r": "4.5.1", "os": "wasm", "version": "1.63.0", "date": "2026-04-30T15:49:56.000Z", "arch": "emscripten", "commit": "8d8c63f53162b2fabd10980c3ac7e77f71e31e9e", "fileid": "8d70a868f59b50d2c76ed7440a2041590e40808c92d03f1c877a4aa3d81c178b", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173438673" }, { "r": "4.7.0", "os": "win", "version": "1.63.0", "date": "2026-04-30T15:40:55.000Z", "arch": "x86_64", "commit": "8d8c63f53162b2fabd10980c3ac7e77f71e31e9e", "fileid": "5fab55dd0b8864ae468506f2cd8d9d033a6894268702620e7fd619156ba901e6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173438673" }, { "r": "4.5.3", "os": "win", "version": "1.63.0", "date": "2026-04-30T15:41:56.000Z", "arch": "x86_64", "commit": "8d8c63f53162b2fabd10980c3ac7e77f71e31e9e", "fileid": "dae041439aee59344217cddff85c37eeb2fe511d2fbf2bdff8363d1869669c4c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173438673" }, { "r": "4.6.0", "os": "win", "version": "1.63.0", "date": "2026-04-30T15:40:41.000Z", "arch": "x86_64", "commit": "8d8c63f53162b2fabd10980c3ac7e77f71e31e9e", "fileid": "fbb118420b347b385f942123d4f1412148d75168e44eda18f36577bf877afc40", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173438673" } ] }