{ "_id": "6a1ae8581d7bb097a09f1ec2", "Package": "R453Plus1Toolbox", "Type": "Package", "Title": "A package for importing and analyzing data from Roche's Genome\nSequencer System", "Version": "1.62.0", "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", "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-release.r-universe.dev", "Date/Publication": "2026-04-28 12:34:56 UTC", "RemoteUrl": "https://github.com/bioc/R453Plus1Toolbox", "RemoteRef": "RELEASE_3_23", "RemoteSha": "495e7e3a5caa721f7af83039441e05e908fa95af", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-30 09:35:28 UTC", "User": "root" }, "MD5sum": "0bf723c460988a6af2ee898fd709c202", "_user": "bioc-release", "_type": "src", "_file": "R453Plus1Toolbox_1.62.0.tar.gz", "_fileid": "47b498a5572217a620156aa38cfe003820e94f736873238d7ab3ebc03e18846d", "_filesize": 1205926, "_sha256": "47b498a5572217a620156aa38cfe003820e94f736873238d7ab3ebc03e18846d", "_created": "2026-05-30T09:35:28.000Z", "_published": "2026-05-30T13:38:32.635Z", "_jobs": [ { "job": 78640066312, "time": 264, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307332936" }, { "job": 78640066328, "time": 460, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7307271543" }, { "job": 78640066340, "time": 544, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307359438" }, { "job": 78640066339, "time": 470, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307272576" }, { "job": 78640066355, "time": 594, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307363798" }, { "job": 78640066338, "time": 261, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7308569090" }, { "job": 78640066332, "time": 615, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7307294178" }, { "job": 78640066333, 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"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", "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 } 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