{ "_id": "6a193f18acfb0bcc41dd5de7", "Package": "ShortRead", "Type": "Package", "Title": "FASTQ input and manipulation", "Version": "1.70.0", "Authors@R": "c(\nperson(\"Bioconductor Package Maintainer\",\nemail = \"maintainer@bioconductor.org\", role = \"cre\"),\nperson(\"Martin\", \"Morgan\", role = \"aut\"),\nperson(\"Michael\", \"Lawrence\", role = \"ctb\"),\nperson(\"Simon\", \"Anders\", role = \"ctb\"),\nperson(\"Rohit\", \"Satyam\", role = \"ctb\",\ncomment = \"Converted Overview.Rnw vignette from Sweave to RMarkdown / HTML.\"),\nperson(\"J\", \"Wokaty\", role = \"ctb\")\n)", "Description": "This package implements sampling, iteration, and input of\nFASTQ files. The package includes functions for filtering and\ntrimming reads, and for generating a quality assessment report.\nData are represented as DNAStringSet-derived objects, and\neasily manipulated for a diversity of purposes. The package\nalso contains legacy support for early single-end, ungapped\nalignment formats.", "License": "Artistic-2.0", "LazyLoad": "yes", "biocViews": "DataImport, Sequencing, QualityControl", "URL": "https://bioconductor.org/packages/ShortRead,\nhttps://github.com/Bioconductor/ShortRead,\nhttps://support.bioconductor.org/tag/ShortRead", "BugReports": "https://github.com/Bioconductor/ShortRead/issues", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libbz2-dev libjpeg-dev liblzma-dev libpng-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:32:53 UTC", "RemoteUrl": "https://github.com/bioc/ShortRead", "RemoteRef": "RELEASE_3_23", "RemoteSha": "ee5a413ff7d5c2de6b8469a100d7042edd919f70", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-29 06:33:53 UTC", "User": "root" }, "Author": "Bioconductor Package Maintainer [cre],\nMartin Morgan [aut],\nMichael Lawrence [ctb],\nSimon Anders [ctb],\nRohit Satyam [ctb] (Converted Overview.Rnw vignette from Sweave to\nRMarkdown / HTML.),\nJ Wokaty [ctb]", "Maintainer": "Bioconductor Package Maintainer ", "MD5sum": "feb4a20eefe20695b744b10a9f0ba26c", "_user": "bioc-release", "_type": "src", "_file": "ShortRead_1.70.0.tar.gz", "_fileid": "f0ef4cece0b4081bade9e9cb09eccaf6ebe4a56c13132e04f01b53b9c49fb30f", "_filesize": 5451648, "_sha256": "f0ef4cece0b4081bade9e9cb09eccaf6ebe4a56c13132e04f01b53b9c49fb30f", "_created": "2026-05-29T06:33:53.000Z", "_published": "2026-05-29T07:24:08.808Z", "_jobs": [ { "job": 78450514367, "time": 234, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7284647834" }, { "job": 78450514390, "time": 343, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "7284671977" }, { "job": 78450514379, "time": 401, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7284685937" }, { "job": 78450514416, "time": 373, "config": "linux-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7284679434" }, { "job": 78450514401, "time": 433, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7284693215" }, { "job": 78450514396, "time": 211, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7285257169" }, { "job": 78450514373, "time": 418, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7285291022" }, { "job": 78450514394, "time": 229, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7285263118" }, { "job": 78450514376, "time": 463, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7285311147" }, { "job": 78449856157, "time": 314, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7284592887" }, { "job": 78450514365, "time": 185, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7284636354" }, { "job": 78450514404, "time": 547, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7284720242" }, { "job": 78450514436, "time": 499, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7284708524" }, { "job": 78450514413, "time": 421, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7284690194" } ], "_bioccheck": { "error": 0, "warning": 3, "note": 17 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621977894", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/ShortRead", "_commit": { "id": "ee5a413ff7d5c2de6b8469a100d7042edd919f70", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379573 }, "_maintainer": { "name": "Bioconductor Package Maintainer", "email": "maintainer@bioconductor.org", "login": "bioconductor-bot", "description": "", "uuid": 11681645 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "BiocGenerics", "version": ">= 0.23.3", "role": "Depends" }, { "package": "BiocParallel", "role": "Depends" }, { "package": "Biostrings", "version": ">= 2.47.6", "role": "Depends" }, { "package": "Rsamtools", "version": ">= 1.31.2", "role": "Depends" }, { "package": "GenomicAlignments", "version": ">= 1.15.6", "role": "Depends" }, { "package": "S4Vectors", "role": "LinkingTo" }, { "package": "IRanges", "role": "LinkingTo" }, { "package": "XVector", "role": "LinkingTo" }, { "package": "Biostrings", "role": "LinkingTo" }, { "package": "Rhtslib", "role": "LinkingTo" }, { "package": "Biobase", "role": "Imports" }, { "package": "S4Vectors", "version": ">= 0.17.25", "role": "Imports" }, { "package": "IRanges", "version": ">= 2.13.12", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "GenomicRanges", "version": ">= 1.31.8", "role": "Imports" }, { "package": "pwalign", "role": "Imports" }, { "package": "hwriter", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "lattice", "role": "Imports" }, { "package": "latticeExtra", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "biomaRt", "role": "Suggests" }, { "package": "GenomicFeatures", "role": "Suggests" }, { "package": "yeastNagalakshmi", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 56, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-44", "n": 3 }, { "week": "2025-45", "n": 1 }, { "week": "2026-10", "n": 1 }, { "week": "2026-16", "n": 4 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.71.0", "bioc": "3.24" }, { "branch": "release", "version": "1.70.0", "bioc": "3.23" } ], "_topics": [ "dataimport", "sequencing", "qualitycontrol", "bioconductor-package", "core-package", "zlib", "cpp" ], "_stars": 8, "_contributors": [ { "user": "mtmorgan", "count": 34, "uuid": 118552 }, { "user": "dtenenba", "count": 25, "uuid": 2286826 }, { "user": "jwokaty", "count": 18, "uuid": 1744257 }, { "user": "hpages", "count": 17, "uuid": 8810451 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "vjcitn", "count": 4, "uuid": 4624066 }, { "user": "sonali-bioc", "count": 2, "uuid": 6373953 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "henrikbengtsson", "count": 1, "uuid": 1616850 }, { "user": "jmacdon", "count": 1, "uuid": 5940924 }, { "user": "kasperdanielhansen", "count": 1, "uuid": 4956575 }, { "user": "kayla-morrell", "count": 1, "uuid": 32339524 }, { "user": "rohit-satyam", "count": 1, "uuid": 55479480 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 11688, "source": "https://www.bioconductor.org/packages/stats/bioc/ShortRead" }, "_mentions": 119, "_devurl": "https://github.com/bioconductor/shortread", "_searchresults": 2160, "_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/ShortRead.html", "manual.pdf" ], "_homeurl": "https://github.com/bioconductor/shortread", "_realowner": "bioc", "_cranurl": false, "_exports": [ "%in%", "alignData", "alignDataFilter", "AlignedDataFrame", "AlignedRead", "alignQuality", "alignQualityFilter", "alphabet", "alphabetByCycle", "alphabetFrequency", "alphabetScore", "analysisPath", "annTrack", "append", "ArrayIntensity", "baseCallPath", "basePath", "chromosome", "chromosomeFilter", "clean", "close.ShortReadFile", "coerce", "compose", "countFastq", "countLines", "coverage", "dataPath", "dustyFilter", "dustyScore", "encoding", "experimentPath", "ExperimentPath", "fac", "FastqFile", "FastqFileList", "FastqQuality", "FastqSampler", "FastqSamplerList", "FastqStreamer", "FastqStreamerList", "files", "filterFastq", "flag", "functions", "getTrellis", "id", "idFilter", "ignore.strand", "imageAnalysisPath", "IntegerQuality", "intensity", "laneDescription", "laneNames", "lapply", "left", "limits", "MatrixQuality", "measurementError", "name", "narrow", "nFilter", "NumericQuality", "occurrenceFilter", "open.ShortReadFile", "pan", "pData", "phenoData", "polyn", "polynFilter", "position", "positionFilter", "qa", "QA", "qa2", "QAAdapterContamination", "QACollate", "QAData", "QAFastqSource", "QAFiltered", "QAFlagged", "QAFrequentSequence", "QANucleotideByCycle", "QANucleotideUse", "QAQualityByCycle", "QAQualityUse", "QAReadQuality", "QASequenceUse", "qualPath", "rbind", "read454", "readAligned", "readBaseQuality", "readBfaToc", "readCount", "readData", "reader", "readFasta", "readFastaQual", "readFastq", "readIndex", "readIntensities", "readIntensityInfo", "readPath", "readPrb", "readQseq", "readQual", "readXStringColumns", "renew", "renewable", "report", "report_html", "restore", "reverse", "reverseComplement", "right", "RochePath", "RocheSet", "RtaIntensity", "runNames", "sapply", "scanPath", "SFastqQuality", "ShortRead", "ShortReadQ", "show", "Snapshot", "SnapshotFunction", "SnapshotFunctionList", "SolexaIntensity", "SolexaIntensityInfo", "solexaPath", "SolexaPath", "SolexaSet", "sourcePath", "SpTrellis", "spViewPerFeature", "srdistance", "srdistanceFilter", "srduplicated", "sread", "SRError", "srFilter", "SRFilterResult", "srlist", "SRList", "srorder", "srrank", "srsort", "SRVector", "SRWarn", "stats", "strand", "strandFilter", "tables", "togglefun", "togglep", "togglez", "trimEnds", "trimLRPatterns", "trimTails", "trimTailw", "uniqueFilter", "varLabels", "varMetadata", "vclass", "view", "viewer", "vrange", "width", "writeFasta", "writeFastq", "yield", "zi", "zo", "zoom" ], "_help": [ { "page": "ShortRead-package", "title": "FASTQ input and manipulation.", "topics": [ "ShortRead-package", ".Roche-class", ".ShortReadBase-class", ".Solexa-class", "append,.ShortReadBase,.ShortReadBase-method", "show,.ShortReadBase-method" ] }, { "page": "dotQA-class", "title": "Virtual class for representing quality assessment results", "topics": [ ".QA-class", "rbind,.QA-method", "show,.QA-method" ] }, { "page": "accessors", "title": "(Legacy) Accessors for ShortRead classes", "topics": [ "accessors", "alignData", "alignQuality", "analysisPath", "baseCallPath", "chromosome", "dataPath", "experimentPath", "imageAnalysisPath", "laneDescription", "laneNames", "position", "scanPath", "solexaPath", "vclass" ] }, { "page": "AlignedDataFrame", "title": "(Legacy) AlignedDataFrame constructor", "topics": [ "AlignedDataFrame" ] }, { "page": "AlignedDataFrame-class", "title": "(Legacy) \"AlignedDataFrame\" representing alignment annotations as a data frame", "topics": [ "AlignedDataFrame-class", "append,AlignedDataFrame,AlignedDataFrame-method" ] }, { "page": "AlignedRead", "title": "(Legacy) Construct objects of class \"AlignedRead\"", "topics": [ "AlignedRead" ] }, { "page": "AlignedRead-class", "title": "(Legacy) \"AlignedRead\" class for aligned short reads", "topics": [ "%in%,AlignedRead,IntegerRangesList-method", "AlignedRead-class", "append,AlignedRead,AlignedRead-method", "chromosome,AlignedRead-method", "coerce,AlignedRead,GAlignments-method", "coerce,AlignedRead,GappedReads-method", "coerce,AlignedRead,GRanges-method", "coerce,AlignedRead,IntegerRangesList-method", "coerce,PairwiseAlignments,AlignedRead-method", "coverage,AlignedRead-method", "detail,AlignedRead-method", "position,AlignedRead-method", "show,AlignedRead-method", "srduplicated,AlignedRead-method", "srorder,AlignedRead-method", "srrank,AlignedRead-method", "strand,AlignedRead-method", "[,AlignedRead,ANY,ANY,ANY-method", "[,AlignedRead,ANY,ANY-method", "[,AlignedRead,ANY,missing,ANY-method", "[,AlignedRead,ANY,missing-method", "[,AlignedRead,missing,ANY,ANY-method", "[,AlignedRead,missing,ANY-method", "[,AlignedRead,missing,missing,ANY-method", "[,AlignedRead,missing,missing-method" ] }, { "page": "alphabetByCycle", "title": "Summarize nucleotide, amino acid, or quality scores by cycle", "topics": [ "alphabetByCycle", "alphabetByCycle,BStringSet-method" ] }, { "page": "alphabetScore", "title": "Efficiently calculate the sum of quality scores across bases", "topics": [ "alphabetScore" ] }, { "page": "BowtieQA-class", "title": "(Legacy) Quality assessment summaries from Bowtie files", "topics": [ "BowtieQA-class", "report,BowtieQA-method", "report_html,BowtieQA-method" ] }, { "page": "clean", "title": "Remove sequences with ambiguous nucleotides from short read classes", "topics": [ "clean", "clean,DNAStringSet-method" ] }, { "page": "countLines", "title": "Count lines in all (text) files in a directory whose file name matches a pattern", "topics": [ "countLines" ] }, { "page": "deprecated", "title": "Deprecated and defunct functions", "topics": [ "basePath", "defunct", "deprecated", "readAligned,BamFile-method", "srapply" ] }, { "page": "dustyScore", "title": "Summarize low-complexity sequences", "topics": [ "dustyScore", "dustyScore,DNAStringSet-method", "dustyScore,ShortRead-method" ] }, { "page": "ExperimentPath-class", "title": "(Legacy) \"ExperimentPath\" class representing a file hierarchy of data files", "topics": [ "detail,ExperimentPath-method", "ExperimentPath", "ExperimentPath-class", "show,ExperimentPath-method" ] }, { "page": "Sampler-class", "title": "Sampling and streaming records from fastq files", "topics": [ "close.ShortReadFile", "countFastq,FastqFile-method", "FastqFile", "FastqFile-class", "FastqFileList", "FastqFileList,ANY-method", "FastqFileList,character-method", "FastqFileList-class", "FastqFileReader-class", "FastqSampler", "FastqSampler-class", "FastqSamplerList", "FastqSamplerList,ANY-method", "FastqSamplerList,character-method", "FastqSamplerList-class", "FastqStreamer", "FastqStreamer,ANY,IRanges-method", "FastqStreamer,ANY,missing-method", "FastqStreamer,ANY,numeric-method", "FastqStreamer-class", "FastqStreamerList", "FastqStreamerList,ANY-method", "FastqStreamerList,character-method", "FastqStreamerList-class", "open.ShortReadFile", "readFastq,FastqFile-method", "ShortReadFile-class", "yield", "yield,FastqFileReader-method", "yield,FastqSampler-method", "yield,FastqStreamer-method" ] }, { "page": "filterFastq", "title": "Filter fastq from one file to another", "topics": [ "filterFastq" ] }, { "page": "Intensity-class", "title": "(Legacy) \"Intensity\", \"IntensityInfo\", and \"IntensityMeasure\" base classes for short read image intensities", "topics": [ "ArrayIntensity", "ArrayIntensity-class", "dim,Intensity-method", "intensity", "Intensity-class", "IntensityInfo-class", "IntensityMeasure-class", "measurementError", "readIntensityInfo", "show,Intensity-method", "show,IntensityMeasure-method", "[,IntensityMeasure,ANY,ANY,ANY-method", "[,IntensityMeasure,ANY,ANY-method", "[,IntensityMeasure,ANY,missing,ANY-method", "[,IntensityMeasure,missing,ANY,ANY-method", "[,IntensityMeasure,missing,missing,ANY-method", "[[,ArrayIntensity,ANY,ANY-method" ] }, { "page": "MAQMapQA-class", "title": "(Legacy) Quality assessment summaries from MAQ map files", "topics": [ "MAQMapQA", "MAQMapQA-class", "report,MAQMapQA-method", "report_html,MAQMapQA-method" ] }, { "page": "qa", "title": "Perform quality assessment on short reads", "topics": [ "qa", "qa,character-method", "qa,list-method" ] }, { "page": "QA-class", "title": "(Updated) classes for representing quality assessment results", "topics": [ ".QA2-class", "QA-class", "QAAdapterContamination-class", "QACollate-class", "QAData-class", "QAFastqSource-class", "QAFiltered-class", "QAFlagged-class", "QAFrequentSequence-class", "QANucleotideByCycle-class", "QANucleotideUse-class", "QAQualityByCycle-class", "QAQualityUse-class", "QAReadQuality-class", "QASequenceUse-class", "QASource-class", "QASummary-class" ] }, { "page": "qa2", "title": "(Updated) quality assessment reports on short reads", "topics": [ "flag", "flag,.QA2-method", "flag,QAFrequentSequence-method", "flag,QAReadQuality-method", "flag,QASource-method", "QA", "qa2", "qa2,FastqSampler-method", "qa2,QAAdapterContamination-method", "qa2,QACollate-method", "qa2,QAFastqSource-method", "qa2,QAFrequentSequence-method", "qa2,QANucleotideByCycle-method", "qa2,QANucleotideUse-method", "qa2,QAQualityByCycle-method", "qa2,QAQualityUse-method", "qa2,QAReadQuality-method", "qa2,QASequenceUse-method", "QAAdapterContamination", "QACollate", "QACollate,missing-method", "QACollate,QAFastqSource-method", "QAData", "QAFastqSource", "QAFiltered", "QAFlagged", "QAFrequentSequence", "QANucleotideByCycle", "QANucleotideUse", "QAQualityByCycle", "QAQualityUse", "QAReadQuality", "QASequenceUse", "rbind,QASummary-method", "report,QA-method", "report,QAAdapterContamination-method", "report,QAFiltered-method", "report,QAFlagged-method", "report,QAFrequentSequence-method", "report,QANucleotideByCycle-method", "report,QANucleotideUse-method", "report,QAQualityByCycle-method", "report,QAQualityUse-method", "report,QAReadQuality-method", "report,QASequenceUse-method", "report,QASource-method", "show,QAAdapterContamination-method", "show,QACollate-method", "show,QAFastqSource-method", "show,QAFrequentSequence-method", "show,QAReadQuality-method", "show,QASummary-method" ] }, { "page": "QualityScore", "title": "Construct objects indicating read or alignment quality", "topics": [ "FastqQuality", "FastqQuality,BStringSet-method", "FastqQuality,character-method", "FastqQuality,missing-method", "IntegerQuality", "MatrixQuality", "NumericQuality", "SFastqQuality", "SFastqQuality,BStringSet-method", "SFastqQuality,character-method", "SFastqQuality,missing-method" ] }, { "page": "QualityScore-class", "title": "Quality scores for short reads and their alignments", "topics": [ "alphabet,FastqQuality-method", "alphabetByCycle,FastqQuality-method", "alphabetFrequency,FastqQuality-method", "alphabetScore,FastqQuality-method", "alphabetScore,PhredQuality-method", "alphabetScore,SFastqQuality-method", "append,MatrixQuality,MatrixQuality-method", "append,QualityScore,QualityScore-method", "coerce,FastqQuality,matrix-method", "coerce,FastqQuality,numeric-method", "coerce,FastqQuality,PhredQuality-method", "coerce,SFastqQuality,matrix-method", "coerce,SFastqQuality,SolexaQuality-method", "detail,QualityScore-method", "dim,MatrixQuality-method", "encoding,FastqQuality-method", "encoding,SFastqQuality-method", "FastqQuality-class", "IntegerQuality-class", "length,MatrixQuality-method", "length,QualityScore-method", "MatrixQuality-class", "narrow,FastqQuality-method", "narrow,MatrixQuality-method", "NumericQuality-class", "QualityScore-class", "reverse,FastqQuality-method", "SFastqQuality-class", "show,FastqQuality-method", "show,NumericQuality-method", "srduplicated,FastqQuality-method", "srorder,FastqQuality-method", "srrank,FastqQuality-method", "srsort,FastqQuality-method", "trimTails,FastqQuality-method", "trimTailw,FastqQuality-method", "width,FastqQuality-method", "width,MatrixQuality-method", "width,NumericQuality-method", "width,QualityScore-method", "[,MatrixQuality,ANY,missing,ANY-method", "[,MatrixQuality,ANY,missing-method", "[,QualityScore,ANY,missing,ANY-method", "[,QualityScore,ANY,missing-method", "[[,MatrixQuality,ANY,missing-method", "[[,QualityScore,ANY,missing-method" ] }, { "page": "readAligned", "title": "(Legacy) Read aligned reads and their quality scores into R representations", "topics": [ "readAligned", "readAligned,character-method" ] }, { "page": "readBaseQuality", "title": "(Legacy) Read short reads and their quality scores into R representations", "topics": [ "readBaseQuality", "readBaseQuality,character-method" ] }, { "page": "readBfaToc", "title": "(Legacy) Get a list of the sequences in a Maq .bfa file", "topics": [ "readBfaToc" ] }, { "page": "readFasta", "title": "Read and write FASTA files to or from ShortRead objects", "topics": [ "readFasta", "readFasta,character-method", "writeFasta", "writeFasta,DNAStringSet-method" ] }, { "page": "readFastq", "title": "Read, write, and count records in FASTQ-formatted files", "topics": [ "countFastq", "countFastq,character-method", "readFastq", "readFastq,character-method", "writeFastq" ] }, { "page": "readIntensities", "title": "(Legacy) Read Illumina image intensity files", "topics": [ "readIntensities", "readIntensities,character-method" ] }, { "page": "readPrb", "title": "(Legacy) Read Solexa prb files as fastq-style quality scores", "topics": [ "readPrb", "readPrb,character-method" ] }, { "page": "readQseq", "title": "(Legacy) Read Solexa qseq files as fastq-style quality scores", "topics": [ "readQseq", "readQseq,character-method" ] }, { "page": "readXStringColumns", "title": "Read one or more columns into XStringSet (e.g., DNAStringSet) objects", "topics": [ "readXStringColumns" ] }, { "page": "renew", "title": "Renew (update) a ShortRead object with new values", "topics": [ "renew", "renew,.ShortReadBase-method", "renewable", "renewable,.ShortReadBase-method", "renewable,character-method", "renewable,missing-method" ] }, { "page": "report", "title": "Summarize quality assessment results into a report", "topics": [ "report", "report,ANY-method", "report_html" ] }, { "page": "RochePath-class", "title": "(Legacy) \"RochePath\" class representing a Roche (454) experiment location", "topics": [ "detail,RochePath-method", "qualPath", "read454", "read454,RochePath-method", "readBaseQuality,RochePath-method", "readFasta,RochePath-method", "readFastaQual", "readFastaQual,character-method", "readFastaQual,RochePath-method", "readPath", "readQual", "readQual,character-method", "readQual,RochePath-method", "RochePath", "RochePath-class", "RocheSet,character-method", "RocheSet,RochePath-method", "runNames", "runNames,RochePath-method", "show,RochePath-method" ] }, { "page": "RocheSet-class", "title": "(Legacy) Roche (454) experiment-wide data container", "topics": [ "RocheSet", "RocheSet-class" ] }, { "page": "RtaIntensity", "title": "(Legacy) Construct objects of class \"RtaIntensity\"", "topics": [ "RtaIntensity" ] }, { "page": "RtaIntensity-class", "title": "(Legacy) Class \"RtaIntensity\"", "topics": [ "RtaIntensity-class" ] }, { "page": "ShortRead-class", "title": "\"ShortRead\" class for short reads", "topics": [ "alphabetByCycle,ShortRead-method", "append,ShortRead,ShortRead-method", "clean,ShortRead-method", "coerce,ShortRead,DNAStringSet-method", "detail,ShortRead-method", "id", "id,ShortRead-method", "length,ShortRead-method", "narrow,ShortRead-method", "ShortRead", "ShortRead,DNAStringSet,BStringSet-method", "ShortRead,DNAStringSet,missing-method", "ShortRead,missing,missing-method", "ShortRead-class", "show,ShortRead-method", "srdistance,ShortRead,ANY-method", "srduplicated,ShortRead-method", "sread", "sread,ShortRead-method", "srorder,ShortRead-method", "srrank,ShortRead-method", "srsort,ShortRead-method", "tables,ShortRead-method", "trimLRPatterns,ShortRead-method", "width,ShortRead-method", "writeFasta,ShortRead-method", "[,ShortRead,ANY,ANY,ANY-method", "[,ShortRead,ANY,ANY-method", "[,ShortRead,ANY,missing,ANY-method", "[,ShortRead,ANY,missing-method", "[,ShortRead,missing,ANY,ANY-method", "[,ShortRead,missing,ANY-method", "[,ShortRead,missing,missing,ANY-method", "[,ShortRead,missing,missing-method" ] }, { "page": "ShortRead-deprecated", "title": "Deprecated functions from the ShortRead package", "topics": [ "uniqueFilter" ] }, { "page": "ShortReadQ-class", "title": "\"ShortReadQ\" class for short reads and their quality scores", "topics": [ "alphabetByCycle,ShortReadQ-method", "alphabetScore,ShortReadQ-method", "append,ShortReadQ,ShortReadQ-method", "coerce,ShortReadQ,QualityScaledDNAStringSet-method", "detail,ShortReadQ-method", "narrow,ShortReadQ-method", "qa,ShortReadQ-method", "reverse,ShortReadQ-method", "reverseComplement,ShortReadQ-method", "ShortReadQ", "ShortReadQ,DNAStringSet,BStringSet,BStringSet-method", "ShortReadQ,DNAStringSet,BStringSet,missing-method", "ShortReadQ,DNAStringSet,QualityScore,BStringSet-method", "ShortReadQ,DNAStringSet,QualityScore,missing-method", "ShortReadQ,missing,missing,missing-method", "ShortReadQ-class", "trimTails,ShortReadQ-method", "trimTailw,ShortReadQ-method", "writeFastq,ShortReadQ,character-method", "writeFastq,ShortReadQ,FastqFile-method", "[,ShortReadQ,ANY,ANY,ANY-method", "[,ShortReadQ,ANY,ANY-method", "[,ShortReadQ,ANY,missing,ANY-method", "[,ShortReadQ,ANY,missing-method", "[,ShortReadQ,missing,ANY,ANY-method", "[,ShortReadQ,missing,ANY-method", "[,ShortReadQ,missing,missing,ANY-method", "[,ShortReadQ,missing,missing-method", "[<-,ShortReadQ,ANY,missing,ShortReadQ-method" ] }, { "page": "FastqQA-class", "title": "Quality assessment of fastq files and ShortReadQ objects", "topics": [ "FastqQA", "FastqQA-class", "report,FastqQA-method", "report_html,FastqQA-method", "report_html,ShortReadQQA-method", "ShortReadQQA-class" ] }, { "page": "Snapshot-class", "title": "Class '\"Snapshot\"'", "topics": [ "annTrack", "annTrack,Snapshot-method", "fac", "fac,Snapshot-method", "files", "files,Snapshot-method", "functions", "functions,Snapshot-method", "getTrellis", "getTrellis,Snapshot-method", "ignore.strand", "ignore.strand,Snapshot-method", "pan", "pan,Snapshot-method", "show,Snapshot-method", "Snapshot", "Snapshot,BamFileList,GRanges-method", "Snapshot,character,GRanges-method", "Snapshot,character,missing-method", "Snapshot-class", "togglefun", "togglefun,Snapshot-method", "togglep", "togglep,Snapshot-method", "togglez", "togglez,Snapshot-method", "trellis-class", "view", "view,Snapshot-method", "vrange", "vrange,Snapshot-method", "zoom", "zoom,Snapshot-method" ] }, { "page": "SnapshotFunction-class", "title": "Class \"SnapshotFunction\"", "topics": [ "limits", "reader", "show,SnapshotFunction-method", "SnapshotFunction", "SnapshotFunction-class", "SnapshotFunctionList", "SnapshotFunctionList,ANY-method", "SnapshotFunctionList,SnapshotFunction-method", "SnapshotFunctionList-class", "viewer" ] }, { "page": "SolexaExportQA-class", "title": "(Legacy) Quality assessment summaries from Solexa export and realign files", "topics": [ "report,SolexaExportQA-method", "report_html,SolexaExportQA-method", "report_html,SolexaRealignQA-method", "show,SolexaExportQA-method", "SolexaExportQA", "SolexaExportQA-class", "SolexaRealignQA-class" ] }, { "page": "SolexaIntensity", "title": "(Legacy) Construct objects of class \"SolexaIntensity\" and \"SolexaIntensityInfo\"", "topics": [ "SolexaIntensity", "SolexaIntensityInfo" ] }, { "page": "SolexaIntensity-class", "title": "Classes \"SolexaIntensity\" and \"SolexaIntensityInfo\"", "topics": [ "SolexaIntensity-class", "SolexaIntensityInfo-class", "[,SolexaIntensity,ANY,ANY,ANY-method", "[,SolexaIntensity,ANY,ANY-method", "[,SolexaIntensity,ANY,missing,ANY-method", "[,SolexaIntensity,missing,ANY,ANY-method", "[,SolexaIntensity,missing,missing,ANY-method" ] }, { "page": "SolexaPath-class", "title": "(Legacy) \"SolexaPath\" class representing a standard output file hierarchy", "topics": [ "detail,SolexaPath-method", "qa,SolexaPath-method", "readAligned,SolexaPath-method", "readBaseQuality,SolexaPath-method", "readFasta,SolexaPath-method", "readFastq,SolexaPath-method", "readIntensities,SolexaPath-method", "readPrb,SolexaPath-method", "readQseq,SolexaPath-method", "report,SolexaPath-method", "show,SolexaPath-method", "SolexaPath", "SolexaPath-class", "SolexaSet,SolexaPath-method" ] }, { "page": "SolexaSet-class", "title": "(Legacy) \"SolexaSet\" coordinating Solexa output locations with sample annotations", "topics": [ "detail,SolexaSet-method", "laneNames,AnnotatedDataFrame-method", "laneNames,SolexaSet-method", "readAligned,SolexaSet-method", "show,SolexaSet-method", "SolexaSet", "SolexaSet,character-method", "SolexaSet-class" ] }, { "page": "SpTrellis-class", "title": "Class \"SpTrellis\"", "topics": [ "left", "left,SpTrellis-method", "restore", "restore,SpTrellis-method", "right", "right,SpTrellis-method", "show,SpTrellis-method", "SpTrellis", "SpTrellis-class", "zi", "zi,SpTrellis-method", "zo", "zo,SpTrellis-method" ] }, { "page": "spViewPerFeature", "title": "Tools to visualize genomic data", "topics": [ "spViewPerFeature" ] }, { "page": "srdistance", "title": "Edit distances between reads and a small number of short references", "topics": [ "srdistance", "srdistance,DNAStringSet,character-method", "srdistance,DNAStringSet,DNAString-method", "srdistance,DNAStringSet,DNAStringSet-method" ] }, { "page": "srduplicated", "title": "Order, sort, and find duplicates in XStringSet objects", "topics": [ "srduplicated", "srduplicated,XStringSet-method", "srorder", "srorder,XStringSet-method", "srrank", "srrank,XStringSet-method", "srsort", "srsort,XStringSet-method" ] }, { "page": "srFilter", "title": "Functions for user-created and built-in ShortRead filters", "topics": [ "alignDataFilter", "alignQualityFilter", "chromosomeFilter", "compose", "dustyFilter", "idFilter", "nFilter", "occurrenceFilter", "polynFilter", "positionFilter", "srdistanceFilter", "srFilter", "srFilter,function-method", "srFilter,missing-method", "strandFilter" ] }, { "page": "SRFilter-class", "title": "\"SRFilter\" for representing functions operating on ShortRead objects", "topics": [ "c,SRFilter-method", "coerce,SRFilter,FilterRules-method", "name", "name,SRFilter-method", "show,SRFilter-method", "srFilter,SRFilter-method", "SRFilter-class" ] }, { "page": "SRFilterResult-class", "title": "\"SRFilterResult\" for SRFilter output and statistics", "topics": [ "!,SRFilterResult-method", "Logic,SRFilterResult,SRFilterResult-method", "name,SRFilterResult-method", "show,SRFilterResult-method", "SRFilterResult", "SRFilterResult-class", "stats", "stats,SRFilterResult-method" ] }, { "page": "SRSet-class", "title": "(Legacy) A base class for Roche experiment-wide data", "topics": [ "detail,SRSet-method", "experimentPath,SRSet-method", "phenoData,SRSet-method", "readCount", "readData", "readIndex", "show,SRSet-method", "sourcePath", "SRSet-class" ] }, { "page": "SRUtil-class", "title": "\".SRUtil\" and related classes", "topics": [ ".SRUtil-class", "detail,.ShortReadBase-method", "detail,SRList-method", "detail,SRVector-method", "lapply,SRList,ANY-method", "lapply,SRList-method", "length,SRList-method", "names,SRList-method", "names<-,SRList,character-method", "sapply,SRList-method", "show,SRList-method", "show,SRVector-method", "SRError", "SRError-class", "SRList", "srlist", "SRList-class", "SRVector", "SRVector-class", "SRWarn", "SRWarn-class", "[,SRList,ANY,missing,ANY-method", "[,SRList,ANY,missing-method", "[[,SRList,ANY,missing-method" ] }, { "page": "tables", "title": "Summarize XStringSet read frequencies", "topics": [ "tables", "tables,XStringSet-method" ] }, { "page": "trimTails", "title": "Trim ends of reads based on nucleotides or qualities", "topics": [ "trimEnds", "trimEnds,character-method", "trimEnds,FastqQuality-method", "trimEnds,ShortRead-method", "trimEnds,ShortReadQ-method", "trimEnds,XStringQuality-method", "trimEnds,XStringSet-method", "trimTails", "trimTails,BStringSet-method", "trimTails,character-method", "trimTails,XStringQuality-method", "trimTailw", "trimTailw,BStringSet-method", "trimTailw,character-method", "trimTailw,XStringQuality-method" ] }, { "page": "polyn", "title": "Utilities for common, simple operations", "topics": [ "polyn" ] } ], "_rundeps": [ "abind", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bitops", "cigarillo", "codetools", "cpp11", "crayon", "DelayedArray", "deldir", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "hwriter", "interp", "IRanges", "jpeg", "lambda.r", "lattice", "latticeExtra", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "png", "pwalign", "RColorBrewer", "Rcpp", "RcppEigen", "Rhtslib", "Rsamtools", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "SummarizedExperiment", "XVector" ], "_sysdeps": [ { "shlib": "libz", "package": "zlib1g", "headers": "zlib1g-dev", "source": "zlib", "version": "1:1.3.dfsg-3.1ubuntu2.1", "name": "zlib", "homepage": "http://zlib.net/", "description": "compression library - runtime" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "Overview.Rmd", "filename": "Overview.html", "title": "An Introduction to ShortRead", "author": "Martin Morgan, Rohit Satyam", "engine": "knitr::rmarkdown", "headings": [ "Sample data", "Functionality", "Common workflows", "Quality assessment", "Filtering and trimming", "Using ShortRead for data exploration", "Data I/O", "readXStringColumns", "Sorting", "Summarizing read occurrence", "Finding near matches to short sequences", "Legacy support for early file formats", "Session Info" ], "created": "2024-01-03 03:00:29", "modified": "2024-04-23 17:46:45", "commits": 2 } ], "_score": 12.387925719226246, "_indexed": false, "_nocasepkg": "shortread", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/ShortRead", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.70.0", "date": "2026-05-29T06:37:53.000Z", "distro": "noble", "arch": "aarch64", "commit": "ee5a413ff7d5c2de6b8469a100d7042edd919f70", "fileid": "fac9b18ece2517e5e3d66c3a5c4db57d0028ce0c69bbf2192da9792b33e62106", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621977894" }, { "r": "4.7.0", "os": "linux", "version": "1.70.0", "date": "2026-05-29T06:37:56.000Z", "distro": "noble", "arch": "x86_64", "commit": "ee5a413ff7d5c2de6b8469a100d7042edd919f70", "fileid": "cbdf8595c2d84416ebb828fae56805f7ada4792dcf89a26622090f236c356ae8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621977894" }, { "r": "4.6.0", "os": "linux", "version": "1.70.0", "date": "2026-05-29T06:38:24.000Z", "distro": "noble", "arch": "aarch64", "commit": "ee5a413ff7d5c2de6b8469a100d7042edd919f70", "fileid": "4b9b5ee16d6d6e3d3e3fe8b28523a8a8126b04f3b1359692f734b97ee09ca8c9", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621977894" }, { "r": "4.6.0", "os": "linux", "version": "1.70.0", "date": "2026-05-29T06:38:50.000Z", "distro": "noble", "arch": "x86_64", "commit": "ee5a413ff7d5c2de6b8469a100d7042edd919f70", "fileid": "1291dc7756487ae3fe978bb02c9bdabefba4b316805cac16d4b9efc06691bf7c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621977894" }, { "r": "4.5.3", "os": "mac", "version": "1.70.0", "date": "2026-05-29T07:18:42.000Z", "arch": "aarch64", "commit": "ee5a413ff7d5c2de6b8469a100d7042edd919f70", "fileid": "68fecca95d3fd122c715fbb7946e529cc5d897966bce27396e3d1ec40cc688c5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621977894" }, { "r": "4.5.3", "os": "mac", "version": "1.70.0", "date": "2026-05-29T07:18:51.000Z", "arch": "x86_64", "commit": "ee5a413ff7d5c2de6b8469a100d7042edd919f70", "fileid": "c4c7fbd335ecbb9e8b2ccd6f8cdea79524c906c106f4b109832adc3d5268738b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621977894" }, { "r": "4.6.0", "os": "mac", "version": "1.70.0", "date": "2026-05-29T07:18:37.000Z", "arch": "aarch64", "commit": "ee5a413ff7d5c2de6b8469a100d7042edd919f70", "fileid": "399d0465bc97ad85df60cad03ce0ed16b6d600a6342b12d7265d38525c3cadca", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621977894" }, { "r": "4.6.0", "os": "mac", "version": "1.70.0", "date": "2026-05-29T07:19:35.000Z", "arch": "x86_64", "commit": "ee5a413ff7d5c2de6b8469a100d7042edd919f70", "fileid": "2578039f24e94107ae8104622c1e5b814c1dc89cbb61e76f7cc8cbc27e54a58f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621977894" }, { "r": "4.6.0", "os": "wasm", "version": "1.70.0", "date": "2026-05-29T06:37:48.000Z", "arch": "emscripten", "commit": "ee5a413ff7d5c2de6b8469a100d7042edd919f70", "fileid": "9c5b5d9d9483baa36fb0737e4482cc6710dae52e9b432ef532474fe23e3cf0e6", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621977894" }, { "r": "4.7.0", "os": "win", "version": "1.70.0", "date": "2026-05-29T06:36:30.000Z", "arch": "x86_64", "commit": "ee5a413ff7d5c2de6b8469a100d7042edd919f70", "fileid": "8469f7faba346e2c637fe62273bce34b1e67018c784d2335aaab81dc4b481db5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621977894" }, { "r": "4.5.3", "os": "win", "version": "1.70.0", "date": "2026-05-29T06:36:12.000Z", "arch": "x86_64", "commit": "ee5a413ff7d5c2de6b8469a100d7042edd919f70", "fileid": "bb8d5c0716e9a89ba2cbfeb8391988c9908186307538844bc62fe31abbc644b4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621977894" }, { "r": "4.6.0", "os": "win", "version": "1.70.0", "date": "2026-05-29T06:36:17.000Z", "arch": "x86_64", "commit": "ee5a413ff7d5c2de6b8469a100d7042edd919f70", "fileid": "95636a06bf5b70813b5e3b683348f3fd2f3fd44a4289ff80c1af18fc64075b71", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621977894" } ] }