{ "_id": "6a4a65881e9cffeb4b83392c", "Package": "R453Plus1Toolbox", "Type": "Package", "Title": "A package for importing and analyzing data from Roche's Genome\nSequencer System", "Version": "1.63.2", "Date": "2026-07-01", "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", "Config/pak/sysreqs": "make libbz2-dev libicu-dev libjpeg-dev liblzma-dev\nlibpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-07-01 19:22:45 UTC", "RemoteUrl": "https://github.com/bioc/R453Plus1Toolbox", "RemoteRef": "HEAD", "RemoteSha": "c022d307efd1aaf48be38fec2fa70d28db3f95c2", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-05 13:57:50 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "R453Plus1Toolbox_1.63.2.tar.gz", "_fileid": "https://r2.ropensci.org/86c96f3149d323d0bc7ac6754a9889f97cd24f20793eac1151a942083ff74e64", "_filesize": 1210187, "_sha256": "86c96f3149d323d0bc7ac6754a9889f97cd24f20793eac1151a942083ff74e64", "_expires": "2026-10-13T14:09:04.000Z", 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"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", 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