{ "_id": "6a1afab81d7bb097a09fc494", "Package": "ShortRead", "Type": "Package", "Title": "FASTQ input and manipulation", "Version": "1.71.0", "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.r-universe.dev", "Date/Publication": "2026-04-28 12:32:53 UTC", "RemoteUrl": "https://github.com/bioc/ShortRead", "RemoteRef": "HEAD", "RemoteSha": "4ea2e0634165830b7e0f5d4e8bd8bb37612568c2", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-30 09:49:22 UTC", "User": "root" }, "Author": "Bioconductor Package Maintainer [cre],\nMartin Morgan [aut],\nMichael Lawrence [ctb],\nSimon Anders [ctb],\nRohit Satyam [ctb] (Converted 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"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": 12.403719986409477, "_indexed": true, "_nocasepkg": "shortread", "_universes": [ "bioc", "bioconductor-bot", "bioconductor" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.71.0", "date": "2026-05-30T09:53:48.000Z", "distro": "noble", "arch": "aarch64", "commit": "4ea2e0634165830b7e0f5d4e8bd8bb37612568c2", "fileid": "a1dd9ad9ec5a1775b16692e870e62dc7fb73327e92a66d6076db787733600846", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677045600" }, { "r": "4.7.0", "os": "linux", "version": "1.71.0", "date": "2026-05-30T10:33:27.000Z", "distro": "noble", "arch": "x86_64", "commit": "4ea2e0634165830b7e0f5d4e8bd8bb37612568c2", "fileid": 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