{ "_id": "6ae73d5b1e2c7b3a4f52fe0e", "Package": "Biostrings", "Title": "Efficient manipulation of biological strings", "Description": "Memory efficient string containers, string matching\nalgorithms, and other utilities, for fast manipulation of large\nbiological sequences or sets of sequences.", "biocViews": "SequenceMatching, Alignment, Sequencing, Genetics,\nDataImport, DataRepresentation, Infrastructure", "URL": "https://bioconductor.org/packages/Biostrings", "BugReports": "https://github.com/Bioconductor/Biostrings/issues", "Version": "2.81.9", "License": "Artistic-2.0", "Encoding": "UTF-8", "Authors@R": "c(\nperson(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"),\nemail=\"hpages.on.github@gmail.com\"),\nperson(\"Patrick\", \"Aboyoun\", role=\"aut\"),\nperson(\"Robert\", \"Gentleman\", role=\"aut\"),\nperson(\"Saikat\", \"DebRoy\", role=\"aut\"),\nperson(\"Vince\", \"Carey\", role=\"ctb\"),\nperson(\"Nicolas\", \"Delhomme\", role=\"ctb\"),\nperson(\"Felix\", \"Ernst\", role=\"ctb\"),\nperson(\"Wolfgang\", \"Huber\", role=\"ctb\",\ncomment=\"'matchprobes' vignette\"),\nperson(\"Haleema\", \"Khan\", role=\"ctb\",\ncomment=\"Converted 'matchprobes' vignette from Sweave to RMarkdown\"),\nperson(\"Aidan\", \"Lakshman\", role=\"ctb\"),\nperson(\"Michael\", \"Lawrence\", role=\"ctb\"),\nperson(\"Kieran\", \"O'Neill\", role=\"ctb\"),\nperson(\"Valerie\", \"Obenchain\", role=\"ctb\"),\nperson(\"Marcel\", \"Ramos\", role=\"ctb\"),\nperson(\"Albert\", \"Vill\", role=\"ctb\"),\nperson(\"Jen\", \"Wokaty\", role=\"ctb\",\ncomment=\"Converted 'matchprobes' vignette from Sweave to RMarkdown\"),\nperson(\"Erik\", \"Wright\", role=\"ctb\"))", "VignetteBuilder": "knitr", "Collate": "utils.R IUPAC_CODE_MAP.R AMINO_ACID_CODE.R GENETIC_CODE.R\nXStringCodec-class.R seqtype.R coloring.R XString-class.R\nXStringSet-class.R XStringSet-comparison.R XStringViews-class.R\nMaskedXString-class.R XStringSetList-class.R seqinfo-methods.R\nxscat.R XStringSet-io.R letter.R getSeq.R letterFrequency.R\ndinucleotideFrequencyTest.R chartr.R reverseComplement.R\ntranslate.R toComplex.R replaceAt.R replaceLetterAt.R\ninjectHardMask.R padAndClip.R strsplit-methods.R misc.R\nMIndex-class.R MIndexList-class.R lowlevel-matching.R\nmatch-utils.R matchPattern.R maskMotif.R matchLRPatterns.R\ntrimLRPatterns.R matchProbePair.R matchPWM.R findPalindromes.R\nPDict-class.R matchPDict.R XStringQuality-class.R\nQualityScaledXStringSet.R lcsuffix.R MultipleAlignment.R\nlongestConsecutive.R predefined_scoring_matrices.R zzz.R", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-09-05 00:04:57 UTC", "RemoteUrl": "https://github.com/bioc/Biostrings", "RemoteRef": "HEAD", "RemoteSha": "fb0cd89830abd054cf2681d6bc6c929981e07b21", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-11-01 12:52:37 UTC", "User": "root" }, "Author": "Hervé Pagès [aut, cre],\nPatrick Aboyoun [aut],\nRobert Gentleman [aut],\nSaikat DebRoy [aut],\nVince Carey [ctb],\nNicolas Delhomme [ctb],\nFelix Ernst [ctb],\nWolfgang Huber [ctb] ('matchprobes' vignette),\nHaleema Khan [ctb] (Converted 'matchprobes' vignette from Sweave to\nRMarkdown),\nAidan Lakshman [ctb],\nMichael Lawrence [ctb],\nKieran O'Neill [ctb],\nValerie Obenchain [ctb],\nMarcel Ramos [ctb],\nAlbert Vill [ctb],\nJen Wokaty [ctb] (Converted 'matchprobes' vignette from Sweave to\nRMarkdown),\nErik Wright [ctb]", "Maintainer": "Hervé Pagès ", "_user": "bioc", "_type": "src", "_file": "Biostrings_2.81.9.tar.gz", "_fileid": "https://r2.ropensci.org/2acb9b9f783d8a22e769f2db030fb095f43223a690e1b4479f21d8a98b05e139", "_filesize": 12720219, "_sha256": "2acb9b9f783d8a22e769f2db030fb095f43223a690e1b4479f21d8a98b05e139", "_expires": "2027-02-09T13:23:36.000Z", "_created": "2026-11-01T12:52:37.000Z", "_published": "2026-11-01T13:23:39.382Z", "_upstream": "https://github.com/bioc/Biostrings", "_status": "success", "_maintainer": { "name": "Hervé Pagès", "email": "hpages.on.github@gmail.com", "login": "hpages", "linkedin": "in/hervé-pagès-5038527", "description": "", "uuid": 8810451 }, "_jobs": [ { "job": 124854129598, "time": 295, "config": "bioc-checks", "r": "4.6.2", "check": "ERROR", "artifact": "13084890635" }, { "job": 124854129741, "time": 528, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "13084452270" }, { "job": 124854129645, "time": 495, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "13084044752" }, { "job": 124854129666, "time": 489, "config": "linux-release-arm64", "r": "4.6.2", "check": "WARNING", "artifact": "13084626795" }, { "job": 124854129713, "time": 665, "config": "linux-release-x86_64", "r": "4.6.2", "check": "WARNING", "artifact": "13084193212" }, { "job": 124854129683, "time": 482, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "13084901969" }, { "job": 124854129639, "time": 714, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "13084458058" }, { "job": 124854129630, "time": 638, "config": "macos-release-arm64", "r": "4.6.2", "check": "WARNING", "artifact": "13084872520" }, { "job": 124854129699, "time": 818, "config": "macos-release-x86_64", "r": "4.6.2", "check": "WARNING", "artifact": "13085261140" }, { "job": 124852650905, "time": 381, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13084262737" }, { "job": 124854129936, "time": 228, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13084511724" }, { "job": 124854129662, "time": 648, "config": "windows-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "13084094990" }, { "job": 124854129686, "time": 509, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "13084392475" }, { "job": 124854129703, "time": 582, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "13085150459" }, { "job": 124854129638, "time": 628, "config": "windows-release-arm64", "r": "4.6.2", "check": "WARNING", "artifact": "13084209505" }, { "job": 124854129659, "time": 475, "config": "windows-release-x86_64", "r": "4.6.2", "check": "WARNING", "artifact": "13084871163" } ], "_bioccheck": { "error": 1, "warning": 7, "note": 20 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41308102081", "_commit": { "id": "fb0cd89830abd054cf2681d6bc6c929981e07b21", "author": "Hervé Pagès ", "committer": "Hervé Pagès ", "message": "Biostrings 2.81.9: Fix issue with as.data.frame.XStringSet(), improve tests\n", "time": 1788566697 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "BiocGenerics", "version": ">= 0.37.0", "role": "Depends" }, { "package": "S4Vectors", "version": ">= 0.27.12", "role": "Depends" }, { "package": "IRanges", "version": ">= 2.47.5", "role": "Depends" }, { "package": "XVector", "version": ">= 0.37.1", "role": "Depends" }, { "package": "Seqinfo", "role": "Depends" }, { "package": "S4Vectors", "role": "LinkingTo" }, { "package": "IRanges", "role": "LinkingTo" }, { "package": "XVector", "role": "LinkingTo" }, { "package": "methods", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "crayon", "role": "Imports" }, { "package": "utils", "role": "Suggests" }, { "package": "graphics", "role": "Suggests" }, { "package": "pwalign", "role": "Suggests" }, { "package": "MultipleAlignment", "role": "Suggests" }, { "package": "BSgenome", "version": ">= 1.13.14", "role": "Suggests" }, { "package": "BSgenome.Celegans.UCSC.ce2", "version": ">= 1.3.11", "role": "Suggests" }, { "package": "BSgenome.Dmelanogaster.UCSC.dm3", "version": ">= 1.3.11", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg18", "role": "Suggests" }, { "package": "drosophila2probe", "role": "Suggests" }, { "package": "hgu95av2probe", "role": "Suggests" }, { "package": "hgu133aprobe", "role": "Suggests" }, { "package": "GenomicFeatures", "version": ">= 1.3.14", "role": "Suggests" }, { "package": "hgu95av2cdf", "role": "Suggests" }, { "package": "affy", "version": ">= 1.41.3", "role": "Suggests" }, { "package": "affydata", "version": ">= 1.11.5", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "covr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1466, "_updates": [ { "week": "2025-44", "n": 4 }, { "week": "2025-45", "n": 2 }, { "week": "2025-51", "n": 1 }, { "week": "2026-02", "n": 2 }, { "week": "2026-10", "n": 1 }, { "week": "2026-18", "n": 7 }, { "week": "2026-21", "n": 1 }, { "week": "2026-23", "n": 1 }, { "week": "2026-26", "n": 3 }, { "week": "2026-27", "n": 2 }, { "week": "2026-29", "n": 2 }, { "week": "2026-31", "n": 1 }, { "week": "2026-35", "n": 2 }, { "week": "2026-36", "n": 3 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.81.9", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "2.80.2", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "sequencematching", "alignment", "sequencing", "genetics", "dataimport", "datarepresentation", "infrastructure", "bioconductor-package", "core-package" ], "_stars": 72, "_contributors": [ { "user": "hpages", "count": 146, "uuid": 8810451 }, { "user": "dtenenba", "count": 25, "uuid": 2286826 }, { "user": "ahl27", "count": 18, "uuid": 30053966 }, { "user": "jwokaty", "count": 18, "uuid": 1744257 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "vjcitn", "count": 6, "uuid": 4624066 }, { "user": "felixernst", "count": 3, "uuid": 17824332 }, { "user": "link-ny", "count": 2, "uuid": 4392950 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "oneillkza", "count": 1, "uuid": 3099991 }, { "user": "digitalwright", "count": 1, "uuid": 6781840 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 482, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 129258, "source": "https://www.bioconductor.org/packages/stats/bioc/Biostrings" }, "_mentions": 220, "_devurl": "https://github.com/bioconductor/biostrings", "_searchresults": 15280, "_abi": { "exports": [ { "key": "Biostrings/include", "hash": "8ae29926c871c67d" }, { "key": "Biostrings::AAString", "hash": "4bdfa54ce1bff7c6" }, { "key": "Biostrings::AAStringSet", "hash": "e9ba549a7f6b97fc" }, { "key": "Biostrings::AAStringSetList", "hash": "82d13dc4c82402a2" }, { "key": "Biostrings::ACtree2", "hash": "f405eaf73e242877" }, { "key": "Biostrings::BString", "hash": "2b9f8d116fb0d0d5" }, { "key": "Biostrings::BStringSet", "hash": "b331ac291ce91bc9" }, { "key": "Biostrings::BStringSetList", "hash": "b5efc83c45801efe" }, { "key": "Biostrings::ByPos_MIndex", "hash": "84ceb7a6cae133ff" }, { "key": "Biostrings::DNAString", "hash": "2a693d06298e058a" }, { "key": "Biostrings::DNAStringSet", "hash": "00fac11a33f652c0" }, { "key": "Biostrings::DNAStringSetList", "hash": "33c8dce728d8f11f" }, { "key": "Biostrings::Dups_OR_NULL", "hash": "2cb1cbce914752fd" }, { "key": "Biostrings::Expanded_TB_PDict", "hash": "90951d2ef67fa315" }, { "key": "Biostrings::IlluminaQuality", "hash": "d57d2074cacc94b6" }, { "key": "Biostrings::IntegerBAB", "hash": "1a13337a730b1266" }, { "key": "Biostrings::MIndex", "hash": "04a14f9f506e2b05" }, { "key": "Biostrings::MIndexList", "hash": "5ecdf4d8ca3bf9f9" }, { "key": "Biostrings::MTB_PDict", "hash": "3c402a34ce2f356e" }, { "key": "Biostrings::MaskedAAString", "hash": "507600192af2e6ff" }, { "key": "Biostrings::MaskedBString", "hash": "b4c393db31b1c4ea" }, { "key": "Biostrings::MaskedDNAString", "hash": "8e24e7bf446197e9" }, { "key": "Biostrings::MaskedRNAString", "hash": "3147d301e3c6b921" }, { "key": "Biostrings::MaskedXString", "hash": "991c8d17e7c101a0" }, { "key": "Biostrings::PDict", "hash": "486d33ea24f3e0dd" }, { "key": "Biostrings::PDict3Parts", "hash": "fd0ffc687a57ccac" }, { "key": "Biostrings::PhredQuality", "hash": "e17b75be6f768dd1" }, { "key": "Biostrings::PreprocessedTB", "hash": "ea51c682417d2877" }, { "key": "Biostrings::QualityScaledAAStringSet", "hash": "d7805f9a07ca1ee1" }, { "key": "Biostrings::QualityScaledBStringSet", "hash": "b3531662f00dc23f" }, { "key": "Biostrings::QualityScaledDNAStringSet", "hash": "cd78d621338cad72" }, { "key": "Biostrings::QualityScaledRNAStringSet", "hash": "8ae5398fc62b8047" }, { "key": "Biostrings::QualityScaledXStringSet", "hash": "813fe7c8f8e960a6" }, { "key": "Biostrings::RNAString", "hash": "6f9db343169d9a8c" }, { "key": "Biostrings::RNAStringSet", "hash": "45061597a0530690" }, { "key": "Biostrings::RNAStringSetList", "hash": "7b418af7b196accf" }, { "key": "Biostrings::SolexaQuality", "hash": "2e022bdc577b3de5" }, { "key": "Biostrings::TB_PDict", "hash": "f15bafa9e85c721f" }, { "key": "Biostrings::Twobit", "hash": "29ce257b4cf8ece9" }, { "key": "Biostrings::XString", "hash": "a6740058aebb7061" }, { "key": "Biostrings::XStringCodec", "hash": "dd286eb2a7106594" }, { "key": "Biostrings::XStringQuality", "hash": "d46400bafc65881f" }, { "key": "Biostrings::XStringSet", "hash": "62feba8ae7f03fac" }, { "key": "Biostrings::XStringSetList", "hash": "a14219ee7d410b8e" }, { "key": "Biostrings::XStringViews", "hash": "2886cc0aac6ab7a5" }, { "key": "Biostrings::_AAdecode()", "hash": "77fffff2debd8d19" }, { "key": "Biostrings::_AAencode()", "hash": "77fffff2debd8d19" }, { "key": "Biostrings::_DNAdecode()", "hash": "77fffff2debd8d19" }, { "key": "Biostrings::_DNAencode()", "hash": "77fffff2debd8d19" }, { "key": "Biostrings::_RNAdecode()", "hash": "77fffff2debd8d19" }, { "key": "Biostrings::_RNAencode()", "hash": "77fffff2debd8d19" }, { "key": "Biostrings::_drop_reported_matches()", "hash": "388b1487601e3384" }, { "key": "Biostrings::_get_XStringSet_length()", "hash": "2a2d7b8a802d4103" }, { "key": "Biostrings::_get_XStringSet_width()", "hash": "33a97ea62b293da6" }, { "key": "Biostrings::_get_elt_from_MIndex_holder()", "hash": "aba8aab321c94ad8" }, { "key": "Biostrings::_get_elt_from_XStringSetList_holder()", "hash": "620d4609746e106d" }, { "key": "Biostrings::_get_elt_from_XStringSet_holder()", "hash": "d3904f3d70da0457" }, { "key": "Biostrings::_get_length_from_MIndex_holder()", "hash": "6c53d04d4f8f01cd" }, { "key": "Biostrings::_get_length_from_XStringSetList_holder()", "hash": "e7c83178ad24bd2f" }, { "key": "Biostrings::_get_length_from_XStringSet_holder()", "hash": "39847a79e8a6358a" }, { "key": "Biostrings::_get_linear_subset_from_XStringSet_holder()", "hash": "324e19a59967b2c7" }, { "key": "Biostrings::_get_match_count()", "hash": "49132affc9735f85" }, { "key": "Biostrings::_get_width0_elt_from_MIndex_holder()", "hash": "b1cf6fe551666439" }, { "key": "Biostrings::_hold_MIndex()", "hash": "8392f5fa3a6887c3" }, { "key": "Biostrings::_hold_XStringSet()", "hash": "db9e2ce9026ca86b" }, { "key": "Biostrings::_hold_XStringSetList()", "hash": "c4d8c526070a0eb8" }, { "key": "Biostrings::_init_match_reporting()", "hash": "1dea78478e9558b9" }, { "key": "Biostrings::_match_pattern_boyermoore()", "hash": "19cdfdd28ddc3222" }, { "key": "Biostrings::_report_match()", "hash": "5bd798f8146bc979" }, { "key": "Biostrings::_reported_matches_asSEXP()", "hash": "c684a9bbe15cdc52" }, { "key": "Biostrings::_set_XStringSet_names()", "hash": "55c0d367bcabfa54" }, { "key": "Biostrings::_set_active_PSpair()", "hash": "aa7e2baadefb2749" }, { "key": "Biostrings::_set_match_shift()", "hash": "aa7e2baadefb2749" }, { "key": "Biostrings::generic:PDict", "hash": "752e511a4645f2f1" }, { "key": "Biostrings::generic:PWM", "hash": "3b6cb384873f4be1" }, { "key": "Biostrings::generic:XString", "hash": "dfe3b3959711576c" }, { "key": "Biostrings::generic:XStringSet", "hash": "fbc8721109713bc2" }, { "key": "Biostrings::generic:alphabet", "hash": "7c1145f64b7e2cb8" }, { "key": "Biostrings::generic:alphabetFrequency", "hash": "8964ae4b155536f8" }, { "key": "Biostrings::generic:codons", "hash": "112489983291a4b3" }, { "key": "Biostrings::generic:complement", "hash": "6ff60e01d76757b0" }, { "key": "Biostrings::generic:computeAllFlinks", "hash": "15f14efed7988801" }, { "key": "Biostrings::generic:consensusMatrix", "hash": "79094af3b0709dde" }, { "key": "Biostrings::generic:consensusString", "hash": "b343f3360c8accb5" }, { "key": "Biostrings::generic:countPDict", "hash": "b43eeff5567b2707" }, { "key": "Biostrings::generic:countPWM", "hash": "31280a0da56cdf4f" }, { "key": "Biostrings::generic:countPattern", "hash": "d35b6faa72e63029" }, { "key": "Biostrings::generic:dinucleotideFrequencyTest", "hash": "17da3ca7be62b17b" }, { "key": "Biostrings::generic:dups", "hash": "eb37aa47bc508b03" }, { "key": "Biostrings::generic:encoding", "hash": "afdc4545e929e657" }, { "key": "Biostrings::generic:endIndex", "hash": "1494edb5ca6b60c0" }, { "key": "Biostrings::generic:extractAt", "hash": "ff078e4de000213a" }, { "key": "Biostrings::generic:extract_character_from_XString_by_positions", "hash": "f249da21a108de83" }, { "key": "Biostrings::generic:extract_character_from_XString_by_ranges", "hash": "07dd416a0fcc5ee9" }, { "key": "Biostrings::generic:findPalindromes", "hash": "ddd05d1ffd2fba48" }, { "key": "Biostrings::generic:getSeq", "hash": "bfae3a92c13aba62" }, { "key": "Biostrings::generic:hasAllFlinks", "hash": "61080562a981454c" }, { "key": "Biostrings::generic:hasOnlyBaseLetters", "hash": "42e40dc6e0d08c9a" }, { "key": "Biostrings::generic:injectHardMask", "hash": "9f032825736266e0" }, { "key": "Biostrings::generic:isMatchingEndingAt", "hash": "6c0a21248f28f5b6" }, { "key": "Biostrings::generic:isMatchingStartingAt", "hash": "36db2be918907d09" }, { "key": "Biostrings::generic:lcprefix", "hash": "c4df813ffcb3bbc9" }, { "key": "Biostrings::generic:lcsuffix", "hash": "0fd9ecfefb29817f" }, { "key": "Biostrings::generic:letter", "hash": "e5b9a154f7c328a2" }, { "key": "Biostrings::generic:letterFrequency", "hash": "c92cca2ab7fa7b8e" }, { "key": "Biostrings::generic:letterFrequencyInSlidingView", "hash": "e2fa926dc792616f" }, { "key": "Biostrings::generic:make_XStringSet_from_strings", "hash": "72a5227bccd6a6bc" }, { "key": "Biostrings::generic:make_XString_from_string", "hash": "ac5d51fbc936dc49" }, { "key": "Biostrings::generic:maskMotif", "hash": "15df2c7ae5f193e2" }, { "key": "Biostrings::generic:masks", "hash": "2c52ee28f208234d" }, { "key": "Biostrings::generic:masks<-", "hash": "44b7bff63b062969" }, { "key": "Biostrings::generic:matchLRPatterns", "hash": "313328476c8adab6" }, { "key": "Biostrings::generic:matchPDict", "hash": "2727ab8a285a99a7" }, { "key": "Biostrings::generic:matchPWM", "hash": "d108e8eb2fc4fc31" }, { "key": "Biostrings::generic:matchPattern", "hash": "2205c403f1d9154e" }, { "key": "Biostrings::generic:matchProbePair", "hash": "70c9ee469abcf5f0" }, { "key": "Biostrings::generic:maxQuality", "hash": "e63d1037be494d17" }, { "key": "Biostrings::generic:maxScore", "hash": "ffc46f8b26335b5b" }, { "key": "Biostrings::generic:maxWeights", "hash": "4a5045cf37472e55" }, { "key": "Biostrings::generic:minQuality", "hash": "080d3f5cad4a1931" }, { "key": "Biostrings::generic:minScore", "hash": "cb3aa5ba9e85dbea" }, { "key": "Biostrings::generic:minWeights", "hash": "63c0c7b262626102" }, { "key": "Biostrings::generic:mismatch", "hash": "15ffb4f6d0547e25" }, { "key": "Biostrings::generic:neditEndingAt", "hash": "8dc294de727f717a" }, { "key": "Biostrings::generic:neditStartingAt", "hash": "351bec97f6da1548" }, { "key": "Biostrings::generic:nmatch", "hash": "5329cec1945cb59d" }, { "key": "Biostrings::generic:nmismatch", "hash": "2b0d4e6f43a9342d" }, { "key": "Biostrings::generic:nnodes", "hash": "ac1e150215729ec7" }, { "key": "Biostrings::generic:nucleotideFrequencyAt", "hash": "3c36c0feed53458f" }, { "key": "Biostrings::generic:offset", "hash": "38f9ec3f5002b249" }, { "key": "Biostrings::generic:oligonucleotideFrequency", "hash": "7e717cfcf39ef923" }, { "key": "Biostrings::generic:p2q", "hash": "e0dd8022b8e5d4a8" }, { "key": "Biostrings::generic:palindromeArmLength", "hash": "e66536983db024b5" }, { "key": "Biostrings::generic:palindromeLeftArm", "hash": "cbcf573c206144f4" }, { "key": "Biostrings::generic:palindromeRightArm", "hash": "b3fdc7a784e3bd5f" }, { "key": "Biostrings::generic:patternFrequency", "hash": "75a501924c10ec82" }, { "key": "Biostrings::generic:q2p", "hash": "f2e7a9ccda2f1728" }, { "key": "Biostrings::generic:quality", "hash": "ffce4719040403d9" }, { "key": "Biostrings::generic:replaceAt", "hash": "671ecd402e3b4e68" }, { "key": "Biostrings::generic:replaceLetterAt", "hash": "703a0191524026ec" }, { "key": "Biostrings::generic:reverseComplement", "hash": "5f23d210f66d43f8" }, { "key": "Biostrings::generic:seqtype", "hash": "d772a1e18d01391b" }, { "key": "Biostrings::generic:seqtype<-", "hash": "faf596cb25e7af99" }, { "key": "Biostrings::generic:startIndex", "hash": "33433afb6807d343" }, { "key": "Biostrings::generic:strsplit", "hash": "a557dcf8e9c4f273" }, { "key": "Biostrings::generic:tb", "hash": "25092e0a883d960f" }, { "key": "Biostrings::generic:tb.width", "hash": "466b5edf7e6c993b" }, { "key": "Biostrings::generic:toComplex", "hash": "a0cff157edca9cb4" }, { "key": "Biostrings::generic:translate", "hash": "3952964e1994e6d9" }, { "key": "Biostrings::generic:trimLRPatterns", "hash": "14f07a0b180287b1" }, { "key": "Biostrings::generic:twoWayAlphabetFrequency", "hash": "d146183fdc25e9b7" }, { "key": "Biostrings::generic:twoWayAlphabetFrequencyByQuality", "hash": "4fe76b4c8a51f48f" }, { "key": "Biostrings::generic:uniqueLetters", "hash": "bf7bad092583dfd7" }, { "key": "Biostrings::generic:unmasked", "hash": "273e54ac4c7e57da" }, { "key": "Biostrings::generic:vcountPDict", "hash": "86fc642e38d3027c" }, { "key": "Biostrings::generic:vcountPattern", "hash": "3feb4637dea6d7b5" }, { "key": "Biostrings::generic:vmatchPDict", "hash": "25f543adcf223506" }, { "key": "Biostrings::generic:vmatchPattern", "hash": "1404dd0b6a5d0ec2" }, { "key": "Biostrings::generic:vwhichPDict", "hash": "e578e4e9b5b4e91a" }, { "key": "Biostrings::generic:which.isMatchingEndingAt", "hash": "742b4e24cd85c229" }, { "key": "Biostrings::generic:which.isMatchingStartingAt", "hash": "e43f025950faee6b" }, { "key": "Biostrings::generic:whichPDict", "hash": "4369f9c24dbc0390" }, { "key": "Biostrings::generic:width0", "hash": "63ad6d1e29099197" }, { "key": "Biostrings::generic:xscodes", "hash": "ee39b4205a2d2031" }, { "key": "Biostrings::probetable", "hash": "933a93233e1f4ddb" } ], "imports": [ { "key": "BiocGenerics::generic:as.data.frame", "hash": "bbe06a14e0191ef5" }, { "key": "BiocGenerics::generic:duplicated", "hash": "677d6f0c28ec6b85" }, { "key": "BiocGenerics::generic:match", "hash": "d6f656cbb258bc6c" }, { "key": "BiocGenerics::generic:updateObject", "hash": "2ce9a5b3171bccbf" }, { "key": "BiocGenerics::generic:width", "hash": "667b5cc67ec1c535" }, { "key": "IRanges::CompressedList", "hash": "b347e8e7407257ee" }, { "key": "IRanges::IRangesList", "hash": "06854f60c513775b" }, { "key": "IRanges::IntegerRanges", "hash": "5b4ab596ecee6c08" }, { "key": "IRanges::IntegerRangesList", "hash": "8833642ab535dfed" }, { "key": "IRanges::IntegerRanges_OR_missing", "hash": "1afaa7442fc98cab" }, { "key": "IRanges::Ranges", "hash": "2ec1451ebae33ae7" }, { "key": "IRanges::RangesList", "hash": "0dc12cc95af5ec4b" }, { "key": "IRanges::Views", "hash": "fd07abf9a6858125" }, { "key": "IRanges::_alloc_IRanges()", "hash": "1911ce2d8bd5f3ec" }, { "key": "IRanges::_copy_IRanges_slots()", "hash": "55c0d367bcabfa54" }, { "key": "IRanges::_get_CompressedList_length()", "hash": "2a2d7b8a802d4103" }, { "key": "IRanges::_get_CompressedList_names()", "hash": "33a97ea62b293da6" }, { "key": "IRanges::_get_CompressedList_partitioning()", "hash": "33a97ea62b293da6" }, { "key": "IRanges::_get_CompressedList_unlistData()", "hash": "33a97ea62b293da6" }, { "key": "IRanges::_get_H2LGrouping_high2low()", "hash": "33a97ea62b293da6" }, { "key": "IRanges::_get_H2LGrouping_low2high()", "hash": "33a97ea62b293da6" }, { "key": "IRanges::_get_IRanges_length()", "hash": "2a2d7b8a802d4103" }, { "key": "IRanges::_get_IRanges_names()", "hash": "33a97ea62b293da6" }, { "key": "IRanges::_get_IRanges_start()", "hash": "33a97ea62b293da6" }, { "key": "IRanges::_get_IRanges_width()", "hash": "33a97ea62b293da6" }, { "key": "IRanges::_get_PartitioningByEnd_end()", "hash": "33a97ea62b293da6" }, { "key": "IRanges::_get_Partitioning_names()", "hash": "33a97ea62b293da6" }, { "key": "IRanges::_get_eltNROWS_from_CompressedIRangesList_holder()", "hash": "4ba35a3a51c1149d" }, { "key": "IRanges::_get_elt_from_CompressedIRangesList_holder()", "hash": "55d6e98c10cfe6f7" }, { "key": "IRanges::_get_elt_from_CompressedIntsList_holder()", "hash": "d3c48ab1e7be6678" }, { "key": "IRanges::_get_end_elt_from_IRanges_holder()", "hash": "1222f133193cc43e" }, { "key": "IRanges::_get_length_from_CompressedIRangesList_holder()", "hash": "c9ee3347cad92c4b" }, { "key": "IRanges::_get_length_from_CompressedIntsList_holder()", "hash": "22e986822b574070" }, { "key": "IRanges::_get_length_from_IRanges_holder()", "hash": "af12ab990d80bbcb" }, { "key": "IRanges::_get_linear_subset_from_IRanges_holder()", "hash": "cc308bb21fa3a8f3" }, { "key": "IRanges::_get_names_elt_from_IRanges_holder()", "hash": "81007d01eb078d5f" }, { "key": "IRanges::_get_start_elt_from_IRanges_holder()", "hash": "1222f133193cc43e" }, { "key": "IRanges::_get_width_elt_from_IRanges_holder()", "hash": "1222f133193cc43e" }, { "key": "IRanges::_hold_CompressedIRangesList()", "hash": "c33027dd5f55fdf9" }, { "key": "IRanges::_hold_CompressedIntegerList()", "hash": "0afe81601b52d618" }, { "key": "IRanges::_hold_IRanges()", "hash": "c87a41ce14f48fa5" }, { "key": "IRanges::_invert_overlap_code()", "hash": "a9923e92cf379bec" }, { "key": "IRanges::_new_CompressedList()", "hash": "8af3c1bf9cdb9454" }, { "key": "IRanges::_new_IRanges()", "hash": "9770ed7ae349657a" }, { "key": "IRanges::_new_IRanges_from_IntPairAE()", "hash": "9a36cd96547d412d" }, { "key": "IRanges::_new_PartitioningByEnd()", "hash": "8af3c1bf9cdb9454" }, { "key": "IRanges::_new_list_of_IRanges_from_IntPairAEAE()", "hash": "2cdb997bc8125e16" }, { "key": "IRanges::_set_IRanges_names()", "hash": "55c0d367bcabfa54" }, { "key": "IRanges::generic:Views", "hash": "460906aa379f7c60" }, { "key": "IRanges::generic:collapse", "hash": "fcbaeaaab5117512" }, { "key": "IRanges::generic:coverage", "hash": "0466e4c6bbe02318" }, { "key": "IRanges::generic:gaps", "hash": "074ed2032bd4fa75" }, { "key": "IRanges::generic:maskedratio", "hash": "3a7a31df59aad004" }, { "key": "IRanges::generic:maskedwidth", "hash": "32933c80b6cf173c" }, { "key": "IRanges::generic:reverse", "hash": "413090ab721b6e16" }, { "key": "IRanges::generic:threebands", "hash": "aa0d10c190bc3614" }, { "key": "IRanges::generic:togrouplength", "hash": "d866eaf6b6833986" }, { "key": "IRanges::generic:windows", "hash": "9e1ab084d05f841e" }, { "key": "S4Vectors::Annotated", "hash": "9b5b8ee6ad9969f8" }, { "key": "S4Vectors::List", "hash": "90a253151dc8db9b" }, { "key": "S4Vectors::Vector", "hash": "09cab0bd77ae353b" }, { "key": "S4Vectors::_CharAEAE_append_string()", "hash": "13431b7793b1a8de" }, { "key": "S4Vectors::_CharAEAE_extend()", "hash": "18e62942f06498a2" }, { "key": "S4Vectors::_CharAEAE_get_nelt()", "hash": "f36268759dfc98a1" }, { "key": "S4Vectors::_CharAEAE_insert_at()", "hash": "faf974caa50ac3b8" }, { "key": "S4Vectors::_CharAEAE_set_nelt()", "hash": "2bc05464f1352f5a" }, { "key": "S4Vectors::_CharAE_append_string()", "hash": "471729b0e3ea3bca" }, { "key": "S4Vectors::_CharAE_delete_at()", "hash": "da3f412a233527b0" }, { "key": "S4Vectors::_CharAE_extend()", "hash": "abce3f4d6b967e3d" }, { "key": "S4Vectors::_CharAE_get_nelt()", "hash": "a30ff44c8e3de529" }, { "key": "S4Vectors::_CharAE_insert_at()", "hash": "eff66dfceab00517" }, { "key": "S4Vectors::_CharAE_set_nelt()", "hash": "3dfa134a2155d880" }, { "key": "S4Vectors::_DoubleAE_append()", "hash": "4eb24195355a6539" }, { "key": "S4Vectors::_DoubleAE_delete_at()", "hash": "afcf29fcdb93dd4d" }, { "key": "S4Vectors::_DoubleAE_extend()", "hash": "9550c8a334ca0473" }, { "key": "S4Vectors::_DoubleAE_get_nelt()", "hash": "59fd749ec209563c" }, { "key": "S4Vectors::_DoubleAE_insert_at()", "hash": "541957b23b94746b" }, { "key": "S4Vectors::_DoubleAE_set_nelt()", "hash": "e58d66f0f1138952" }, { "key": "S4Vectors::_DoubleAE_set_val()", "hash": "40e42d8e8417c4d4" }, { "key": "S4Vectors::_IntAEAE_extend()", "hash": "510df193423aa99e" }, { "key": "S4Vectors::_IntAEAE_get_nelt()", "hash": "5bdcf4ce2d6891c7" }, { "key": "S4Vectors::_IntAEAE_insert_at()", "hash": "792a59cf48447da1" }, { "key": "S4Vectors::_IntAEAE_pappend()", "hash": "24d6304bdb0d90f0" }, { "key": "S4Vectors::_IntAEAE_set_nelt()", "hash": "10fcdee5d7174505" }, { "key": "S4Vectors::_IntAEAE_shift()", "hash": "101e82d192fc711d" }, { "key": "S4Vectors::_IntAEAE_sum_and_shift()", "hash": "76a990392af34e1c" }, { "key": "S4Vectors::_IntAEAE_toEnvir()", "hash": "daf8d8f4b6c99422" }, { "key": "S4Vectors::_IntAE_append()", "hash": "4c2761aebc1d5fec" }, { "key": "S4Vectors::_IntAE_delete_at()", "hash": "969ea28fb73f305a" }, { "key": "S4Vectors::_IntAE_extend()", "hash": "cd867721e5f3fccd" }, { "key": "S4Vectors::_IntAE_get_nelt()", "hash": "e6ccbfc4abab24bf" }, { "key": "S4Vectors::_IntAE_insert_at()", "hash": "e69e1abe3dbf914d" }, { "key": "S4Vectors::_IntAE_qsort()", "hash": "e69e1abe3dbf914d" }, { "key": "S4Vectors::_IntAE_set_nelt()", "hash": "0df28f925a5c4ec8" }, { "key": "S4Vectors::_IntAE_set_val()", "hash": "4680cd2717c09f4a" }, { "key": "S4Vectors::_IntAE_shift()", "hash": "e69e1abe3dbf914d" }, { "key": "S4Vectors::_IntAE_sum_and_shift()", "hash": "144ac9e9e2cc7508" }, { "key": "S4Vectors::_IntAE_uniq()", "hash": "cd867721e5f3fccd" }, { "key": "S4Vectors::_IntPairAEAE_extend()", "hash": "4e98facc8fa2c8e1" }, { "key": "S4Vectors::_IntPairAEAE_get_nelt()", "hash": "6863a3053c3829d9" }, { "key": "S4Vectors::_IntPairAEAE_insert_at()", "hash": "73de3765a0dfae83" }, { "key": "S4Vectors::_IntPairAEAE_set_nelt()", "hash": "14de73cca150a220" }, { "key": "S4Vectors::_IntPairAE_extend()", "hash": "d3f8be207fae9f2a" }, { "key": "S4Vectors::_IntPairAE_get_nelt()", "hash": "3c4e764eb15ec77b" }, { "key": "S4Vectors::_IntPairAE_insert_at()", "hash": "1924e2adb94d5bb2" }, { "key": "S4Vectors::_IntPairAE_set_nelt()", "hash": "45f5048929d0fb90" }, { "key": "S4Vectors::_LLongAEAE_extend()", "hash": "d35990f45183c900" }, { "key": "S4Vectors::_LLongAEAE_get_nelt()", "hash": "d85effaf212aeda6" }, { "key": "S4Vectors::_LLongAEAE_insert_at()", "hash": "78e77a9210edb2c4" }, { "key": "S4Vectors::_LLongAEAE_set_nelt()", "hash": "1642b058a064223d" }, { "key": "S4Vectors::_LLongAE_extend()", "hash": "b37ca08df6c28ac7" }, { "key": "S4Vectors::_LLongAE_get_nelt()", "hash": "7660f63a4e462d4e" }, { "key": "S4Vectors::_LLongAE_insert_at()", "hash": "8bb57509e98d8541" }, { "key": "S4Vectors::_LLongAE_set_nelt()", "hash": "715f5812b4e706da" }, { "key": "S4Vectors::_LLongAE_set_val()", "hash": "647bfc6857754ea7" }, { "key": "S4Vectors::_alloc_LLint()", "hash": "0426b4ceb8bf9f6e" }, { "key": "S4Vectors::_as_int()", "hash": "d3d9ddf35cde8eac" }, { "key": "S4Vectors::_check_integer_pairs()", "hash": "f33ababe7813b609" }, { "key": "S4Vectors::_construct_Rle()", "hash": "628a93a3f98ea6d7" }, { "key": "S4Vectors::_construct_character_Rle()", "hash": "628a93a3f98ea6d7" }, { "key": "S4Vectors::_construct_complex_Rle()", "hash": "1d7a89fc89ebd9a0" }, { "key": "S4Vectors::_construct_integer_Rle()", "hash": "d4d0ed89d98172a3" }, { "key": "S4Vectors::_construct_logical_Rle()", "hash": "d4d0ed89d98172a3" }, { "key": "S4Vectors::_construct_numeric_Rle()", "hash": "c0f1f8b29a528f3a" }, { "key": "S4Vectors::_construct_raw_Rle()", "hash": "646533d3e2dcec2d" }, { "key": "S4Vectors::_copy_vector_block()", "hash": "8e80cf4b873414a6" }, { "key": "S4Vectors::_copy_vector_positions()", "hash": "942d1590e048b9e8" }, { "key": "S4Vectors::_copy_vector_ranges()", "hash": "84e775dbe3766f91" }, { "key": "S4Vectors::_extract_bytes_by_positions()", "hash": "ee51db3f938d32d1" }, { "key": "S4Vectors::_extract_bytes_by_ranges()", "hash": "750071c798c79e77" }, { "key": "S4Vectors::_find_interv_and_start_from_width()", "hash": "788dd9d6bd3a2b26" }, { "key": "S4Vectors::_get_LLint_dataptr()", "hash": "5e954df7b6a61e64" }, { "key": "S4Vectors::_get_LLint_length()", "hash": "f8f171bf7848e073" }, { "key": "S4Vectors::_get_List_elementType()", "hash": "b9506dcc532aefab" }, { "key": "S4Vectors::_get_classname()", "hash": "b9506dcc532aefab" }, { "key": "S4Vectors::_get_hbucket_val()", "hash": "55a6c2cf39202a32" }, { "key": "S4Vectors::_get_matches_of_ordered_int_pairs()", "hash": "30fa6ed1f10b6e89" }, { "key": "S4Vectors::_get_matches_of_ordered_int_quads()", "hash": "91a9f2a0f6c46d84" }, { "key": "S4Vectors::_get_order_of_int_array()", "hash": "253fc8781f8e04fe" }, { "key": "S4Vectors::_get_order_of_int_pairs()", "hash": "5ce07f0a1094e7c1" }, { "key": "S4Vectors::_get_order_of_int_quads()", "hash": "b5bdd8e84beeadd3" }, { "key": "S4Vectors::_get_ovflow_flag()", "hash": "49132affc9735f85" }, { "key": "S4Vectors::_get_select_mode()", "hash": "2a2d7b8a802d4103" }, { "key": "S4Vectors::_increase_buflength()", "hash": "92fd0ab51072e5f8" }, { "key": "S4Vectors::_is_LLint()", "hash": "2a2d7b8a802d4103" }, { "key": "S4Vectors::_list_as_data_frame()", "hash": "89b500ce8b4be99c" }, { "key": "S4Vectors::_new_CHARACTER_from_CharAEAE()", "hash": "a0a90c285ae8b59a" }, { "key": "S4Vectors::_new_CHARSXP_from_CharAE()", "hash": "6a5a88f3fcd71421" }, { "key": "S4Vectors::_new_CharAE()", "hash": "2beed20ab90ca70b" }, { "key": "S4Vectors::_new_CharAEAE()", "hash": "67a632c3c222ca98" }, { "key": "S4Vectors::_new_CharAE_from_string()", "hash": "2c761bf84d430b98" }, { "key": "S4Vectors::_new_DFrame()", "hash": "9770ed7ae349657a" }, { "key": "S4Vectors::_new_DoubleAE()", "hash": "66a220193169a4a9" }, { "key": "S4Vectors::_new_DoubleAE_from_NUMERIC()", "hash": "cf931e14afa23b4e" }, { "key": "S4Vectors::_new_Hits()", "hash": "fd5fd548c642ffb3" }, { "key": "S4Vectors::_new_INTEGER_from_IntAE()", "hash": "3ad99796a4e7e924" }, { "key": "S4Vectors::_new_IntAE()", "hash": "26bbe984d9003e07" }, { "key": "S4Vectors::_new_IntAEAE()", "hash": "44d17e547c25cb1e" }, { "key": "S4Vectors::_new_IntAEAE_from_LIST()", "hash": "eed4c1c68c9b4549" }, { "key": "S4Vectors::_new_IntAE_from_CHARACTER()", "hash": "5ac510ce80092446" }, { "key": "S4Vectors::_new_IntAE_from_INTEGER()", "hash": "13653d967df40eb7" }, { "key": "S4Vectors::_new_IntPairAE()", "hash": "1f547cf8631181e8" }, { "key": "S4Vectors::_new_IntPairAEAE()", "hash": "c2f8e37c13f64778" }, { "key": "S4Vectors::_new_LIST_from_IntAEAE()", "hash": "6c038869c083a87d" }, { "key": "S4Vectors::_new_LLongAE()", "hash": "f440a21d72dbee29" }, { "key": "S4Vectors::_new_LLongAEAE()", "hash": "69327110876a161f" }, { "key": "S4Vectors::_new_LOGICAL_from_CharAE()", "hash": "6a5a88f3fcd71421" }, { "key": "S4Vectors::_new_LOGICAL_from_IntAE()", "hash": "3ad99796a4e7e924" }, { "key": "S4Vectors::_new_NUMERIC_from_DoubleAE()", "hash": "29321c85cdb30bb7" }, { "key": "S4Vectors::_new_RAW_from_CharAE()", "hash": "6a5a88f3fcd71421" }, { "key": "S4Vectors::_new_SimpleList()", "hash": "5ff10e460b4147ef" }, { "key": "S4Vectors::_new_SortedByQueryHits_from_IntAEAE()", "hash": "1e648fe983766ae8" }, { "key": "S4Vectors::_new_htab()", "hash": "4e71b39d9fa542ec" }, { "key": "S4Vectors::_positions_mapper()", "hash": "8404d1021181e1ba" }, { "key": "S4Vectors::_ranges_mapper()", "hash": "c6ec4580e7c2bf18" }, { "key": "S4Vectors::_reset_ovflow_flag()", "hash": "388b1487601e3384" }, { "key": "S4Vectors::_safe_int_add()", "hash": "9308f4fd74866595" }, { "key": "S4Vectors::_safe_int_mult()", "hash": "9308f4fd74866595" }, { "key": "S4Vectors::_safe_llint_add()", "hash": "c00db841cec8fd28" }, { "key": "S4Vectors::_safe_llint_mult()", "hash": "c00db841cec8fd28" }, { "key": "S4Vectors::_set_List_elementType()", "hash": "904db26a2e5c6a91" }, { "key": "S4Vectors::_set_hbucket_val()", "hash": "89b238a9c2d06d6e" }, { "key": "S4Vectors::_sort_int_array()", "hash": "ca22adce8021b348" }, { "key": "S4Vectors::_sort_int_pairs()", "hash": "9e4a66813f99b8c5" }, { "key": "S4Vectors::_sort_ints()", "hash": "941c6720e08a1a6a" }, { "key": "S4Vectors::_vector_memcmp()", "hash": "f28d93135432aa51" }, { "key": "S4Vectors::generic:elementNROWS", "hash": "27e9feb3fa9164e1" }, { "key": "S4Vectors::generic:extractROWS", "hash": "f13b9aced5b29924" }, { "key": "S4Vectors::generic:parallel_slot_names", "hash": "7aa17c47f005eef5" }, { "key": "S4Vectors::generic:pcompare", "hash": "c1f78a43d9fdca64" }, { "key": "S4Vectors::generic:pcompareRecursively", "hash": "b20f2a279c59d234" }, { "key": "S4Vectors::generic:relistToClass", "hash": "5c47e2ea0d77491c" }, { "key": "S4Vectors::generic:showAsCell", "hash": "397c9f2858491f2e" }, { "key": "S4Vectors::generic:unstrsplit", "hash": "929608f33e1aaac6" }, { "key": "S4Vectors::list_OR_List", "hash": "fcd6e1f6a8d39f9c" }, { "key": "S4Vectors::vector_OR_Vector", "hash": "f3fc18c9f8ff2633" }, { "key": "Seqinfo::generic:seqinfo", "hash": "1eb5bbe2fff73b75" }, { "key": "Seqinfo::generic:seqinfo<-", "hash": "3818365f39e745d0" }, { "key": "XVector::XRaw", "hash": "1404b7bf29b06e64" }, { "key": "XVector::XRawList", "hash": "d1ed6dc2e090e447" }, { "key": "XVector::XVector", "hash": "5bb0a849aa44419f" }, { "key": "XVector::XVectorList", "hash": "8a649fd5f0c797f7" }, { "key": "XVector::_Ocopy_byteblocks_from_i1i2()", "hash": "9f4dfd63856356b8" }, { "key": "XVector::_Ocopy_byteblocks_from_subscript()", "hash": "37b24366191e9918" }, { "key": "XVector::_Ocopy_byteblocks_to_i1i2()", "hash": "9f4dfd63856356b8" }, { "key": "XVector::_Ocopy_byteblocks_to_subscript()", "hash": "37b24366191e9918" }, { "key": "XVector::_Ocopy_bytes_from_i1i2_to_complex()", "hash": "5c6ea52bd2357ee1" }, { "key": "XVector::_Ocopy_bytes_from_i1i2_with_lkup()", "hash": "bf4a9b030d281005" }, { "key": "XVector::_Ocopy_bytes_from_subscript_with_lkup()", "hash": "0fbd653f5337a41e" }, { "key": "XVector::_Ocopy_bytes_to_i1i2_with_lkup()", "hash": "bf4a9b030d281005" }, { "key": "XVector::_Ocopy_bytes_to_subscript_with_lkup()", "hash": "0fbd653f5337a41e" }, { "key": "XVector::_Orevcopy_byteblocks_from_i1i2()", "hash": "9f4dfd63856356b8" }, { "key": "XVector::_Orevcopy_bytes_from_i1i2_with_lkup()", "hash": "bf4a9b030d281005" }, { "key": "XVector::_alloc_XDouble()", "hash": "1911ce2d8bd5f3ec" }, { "key": "XVector::_alloc_XDoubleList()", "hash": "e80a44059526499d" }, { "key": "XVector::_alloc_XInteger()", "hash": "1911ce2d8bd5f3ec" }, { "key": "XVector::_alloc_XIntegerList()", "hash": "e80a44059526499d" }, { "key": "XVector::_alloc_XRaw()", "hash": "1911ce2d8bd5f3ec" }, { "key": "XVector::_alloc_XRawList()", "hash": "e80a44059526499d" }, { "key": "XVector::_delete_trailing_LF_or_CRLF()", "hash": "d3d9ddf35cde8eac" }, { "key": "XVector::_filexp_fwrite()", "hash": "3637683a4d067b05" }, { "key": "XVector::_filexp_gets()", "hash": "a551ba9f1f73645f" }, { "key": "XVector::_filexp_putc()", "hash": "455127f85d56f714" }, { "key": "XVector::_filexp_puts()", "hash": "78e2ed6064e4376f" }, { "key": "XVector::_filexp_read()", "hash": "ed44fd7b43e66c09" }, { "key": "XVector::_filexp_rewind()", "hash": "63d26947ba7e1377" }, { "key": "XVector::_filexp_seek()", "hash": "8b7ae9a1f137c15a" }, { "key": "XVector::_filexp_tell()", "hash": "f8f171bf7848e073" }, { "key": "XVector::_get_SharedVector_length()", "hash": "2a2d7b8a802d4103" }, { "key": "XVector::_get_SharedVector_tag()", "hash": "33a97ea62b293da6" }, { "key": "XVector::_get_XVectorList_length()", "hash": "2a2d7b8a802d4103" }, { "key": "XVector::_get_XVectorList_names()", "hash": "33a97ea62b293da6" }, { "key": "XVector::_get_XVectorList_width()", "hash": "33a97ea62b293da6" }, { "key": "XVector::_get_XVector_length()", "hash": "2a2d7b8a802d4103" }, { "key": "XVector::_get_XVector_offset()", "hash": "2a2d7b8a802d4103" }, { "key": "XVector::_get_XVector_shared()", "hash": "33a97ea62b293da6" }, { "key": "XVector::_get_XVector_tag()", "hash": "33a97ea62b293da6" }, { "key": "XVector::_get_elt_from_XDoubleList_holder()", "hash": "d6e42c5e0aa8e8f0" }, { "key": "XVector::_get_elt_from_XIntegerList_holder()", "hash": "57231a9ceb0a6ca2" }, { "key": "XVector::_get_elt_from_XRawList_holder()", "hash": "d3904f3d70da0457" }, { "key": "XVector::_get_length_from_XVectorList_holder()", "hash": "39847a79e8a6358a" }, { "key": "XVector::_get_linear_subset_from_XVectorList_holder()", "hash": "324e19a59967b2c7" }, { "key": "XVector::_hold_XDouble()", "hash": "29f07163a38e7677" }, { "key": "XVector::_hold_XInteger()", "hash": "6f89fa0e397a5c24" }, { "key": "XVector::_hold_XRaw()", "hash": "4e0bf52c57d6e98c" }, { "key": "XVector::_hold_XVectorList()", "hash": "db9e2ce9026ca86b" }, { "key": "XVector::_new_SharedVector()", "hash": "5ff10e460b4147ef" }, { "key": "XVector::_new_XDoubleList_from_tag()", "hash": "e8053dd7d7a9199d" }, { "key": "XVector::_new_XDoubleList_from_tags()", "hash": "873fd652b3ff3181" }, { "key": "XVector::_new_XDouble_from_tag()", "hash": "5ff10e460b4147ef" }, { "key": "XVector::_new_XIntegerList_from_IntAEAE()", "hash": "1062cf64543bb87f" }, { "key": "XVector::_new_XIntegerList_from_tag()", "hash": "e8053dd7d7a9199d" }, { "key": "XVector::_new_XIntegerList_from_tags()", "hash": "873fd652b3ff3181" }, { "key": "XVector::_new_XInteger_from_tag()", "hash": "5ff10e460b4147ef" }, { "key": "XVector::_new_XRawList_from_CharAEAE()", "hash": "3cc8ed7c2b0c6660" }, { "key": "XVector::_new_XRawList_from_tag()", "hash": "e8053dd7d7a9199d" }, { "key": "XVector::_new_XRawList_from_tags()", "hash": "873fd652b3ff3181" }, { "key": "XVector::_new_XRaw_from_tag()", "hash": "5ff10e460b4147ef" }, { "key": "XVector::_new_XVector()", "hash": "a3d4acdbc213ab16" }, { "key": "XVector::_set_XVectorList_names()", "hash": "55c0d367bcabfa54" }, { "key": "XVector::generic:subseq", "hash": "0845f0328bac9571" }, { "key": "XVector::generic:subseq<-", "hash": "8bea2b99e2a0bec5" } ] }, "_rbuild": "4.6.2", "_assets": [ "extra/Biostrings.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/bioconductor/biostrings", "_realowner": "bioc", "_cranurl": false, "_exports": [ ".inplaceReplaceLetterAt", "%in%", "AA_ALPHABET", "AA_PROTEINOGENIC", "AA_STANDARD", "AAMultipleAlignment", "AAString", "AAStringSet", "AAStringSetList", "alphabet", "alphabetFrequency", "AMINO_ACID_CODE", "as.data.frame", "as.data.frame.XStringSet", "as.data.frame.XStringViews", "as.list", "as.matrix", "BString", "BStringSet", "BStringSetList", "chartr", "codons", "coerce", "collapse", "colmask", "colmask<-", "Compare", "complement", "computeAllFlinks", "consensusMatrix", "consensusString", "consensusViews", "countPattern", "countPDict", "countPWM", "coverage", "dinucleotideFrequency", "dinucleotideFrequencyTest", "DNA_ALPHABET", "DNA_BASES", "DNAMultipleAlignment", "DNAString", "DNAStringSet", "DNAStringSetList", "duplicated", "encoding", "end", "endIndex", "extract_character_from_XString_by_positions", "extract_character_from_XString_by_ranges", "extractAllMatches", "extractAt", "fasta.index", "fasta.seqlengths", "fastq.geometry", "fastq.seqlengths", "findPalindromes", "gaps", "GENETIC_CODE", "GENETIC_CODE_TABLE", "get_seqtype_conversion_lookup", "getGeneticCode", "getSeq", "gregexpr2", "hasAllFlinks", "hasLetterAt", "hasOnlyBaseLetters", "head", "IlluminaQuality", "initialize", "injectHardMask", "intersect", "is.unsorted", "isMatchingAt", "isMatchingEndingAt", "isMatchingStartingAt", "IUPAC_CODE_MAP", "lcprefix", "lcsuffix", "letter", "letterFrequency", "letterFrequencyInSlidingView", "longestConsecutive", "make_XString_from_string", "make_XStringSet_from_strings", "mask", "maskeddim", "maskedncol", "maskednrow", "maskedratio", "maskedwidth", "maskGaps", "maskMotif", "masks", "masks<-", "match", "matchLRPatterns", "matchPattern", "matchPDict", "matchProbePair", "matchPWM", "maxScore", "maxWeights", "mergeIUPACLetters", "minScore", "minWeights", "mismatch", "mkAllStrings", "N50", "nchar", "neditAt", "neditEndingAt", "neditStartingAt", "nmatch", "nmismatch", "nnodes", "nucleotideFrequencyAt", "oligonucleotideFrequency", "oligonucleotideTransitions", "order", "padAndClip", "palindromeArmLength", "palindromeLeftArm", "palindromeRightArm", "parallel_slot_names", "parallelVectorNames", "patternFrequency", "pcompare", "PDict", "PhredQuality", "PWM", "PWMscoreStartingAt", "quality", "QualityScaledAAStringSet", "QualityScaledBStringSet", "QualityScaledDNAStringSet", "QualityScaledRNAStringSet", "rank", "readAAMultipleAlignment", "readAAStringSet", "readBStringSet", "readDNAMultipleAlignment", "readDNAStringSet", "readQualityScaledDNAStringSet", "readRNAMultipleAlignment", "readRNAStringSet", "relistToClass", "replaceAmbiguities", "replaceAt", "replaceLetterAt", "reverse", "reverseComplement", "RNA_ALPHABET", "RNA_BASES", "RNA_GENETIC_CODE", "RNAMultipleAlignment", "RNAString", "RNAStringSet", "RNAStringSetList", "rowmask", "rowmask<-", "saveXStringSet", "seqinfo", "seqinfo<-", "seqtype", "seqtype<-", "setdiff", "setequal", "show", "showAsCell", "SolexaQuality", "sort", "stackStrings", "start", "startIndex", "strsplit", "subseq", "subseq<-", "substr", "substring", "summary", "tail", "tb", "tb.width", "threebands", "toComplex", "toString", "translate", "trimLRPatterns", "trinucleotideFrequency", "twoWayAlphabetFrequency", "union", "uniqueLetters", "unitScale", "unmasked", "unstrsplit", "update_AA_palette", "update_B_palette", "update_DNA_palette", "update_RNA_palette", "updateObject", "vcountPattern", "vcountPDict", "Views", "vmatchPattern", "vmatchPDict", "vwhichPDict", "which.isMatchingAt", "which.isMatchingEndingAt", "which.isMatchingStartingAt", "whichPDict", "width", "width0", "windows", "write.phylip", "writeQualityScaledXStringSet", "writeXStringSet", "xscat", "xscodes" ], "_datasets": [ { "name": "BLOSUM100", "title": "Predefined scoring matrices", "object": "BLOSUM100", "file": "BLOSUM100.rda", "class": [ "moved_to_pwalign_pkg", "matrix", "array" ], "fields": [ "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "*" ], "rows": 24, "table": true, "tojson": true }, { "name": "BLOSUM45", "title": "Predefined scoring matrices", "object": "BLOSUM45", "file": "BLOSUM45.rda", "class": [ "moved_to_pwalign_pkg", "matrix", "array" ], "fields": [ "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "J", "Z", "X", "*" ], "rows": 25, "table": true, "tojson": true }, { "name": "BLOSUM50", "title": "Predefined scoring matrices", "object": "BLOSUM50", "file": "BLOSUM50.rda", "class": [ "moved_to_pwalign_pkg", "matrix", "array" ], "fields": [ "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "*" ], "rows": 24, "table": true, "tojson": true }, { "name": "BLOSUM62", "title": "Predefined scoring matrices", "object": "BLOSUM62", "file": "BLOSUM62.rda", "class": [ "moved_to_pwalign_pkg", "matrix", "array" ], "fields": [ "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "J", "Z", "X", "*" ], "rows": 25, "table": true, "tojson": true }, { "name": "BLOSUM80", "title": "Predefined scoring matrices", "object": "BLOSUM80", "file": "BLOSUM80.rda", "class": [ "moved_to_pwalign_pkg", "matrix", "array" ], "fields": [ "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "J", "Z", "X", "*" ], "rows": 25, "table": true, "tojson": true }, { "name": "HNF4alpha", "title": "Known HNF4alpha binding sequences", "object": "HNF4alpha", "file": "HNF4alpha.rda", "class": [ "DNAStringSet" ], "fields": [], "table": false, "tojson": false }, { "name": "PAM120", "title": "Predefined scoring matrices", "object": "PAM120", "file": "PAM120.rda", "class": [ "moved_to_pwalign_pkg", "matrix", "array" ], "fields": [ "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "*" ], "rows": 24, "table": true, "tojson": true }, { "name": "PAM250", "title": "Predefined scoring matrices", "object": "PAM250", "file": "PAM250.rda", "class": [ "moved_to_pwalign_pkg", "matrix", "array" ], "fields": [ "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "*" ], "rows": 24, "table": true, "tojson": true }, { "name": "PAM30", "title": "Predefined scoring matrices", "object": "PAM30", "file": "PAM30.rda", "class": [ "moved_to_pwalign_pkg", "matrix", "array" ], "fields": [ "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "J", "Z", "X", "*" ], "rows": 25, "table": true, "tojson": true }, { "name": "PAM40", "title": "Predefined scoring matrices", "object": "PAM40", "file": "PAM40.rda", "class": [ "moved_to_pwalign_pkg", "matrix", "array" ], "fields": [ "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "*" ], "rows": 24, "table": true, "tojson": true }, { "name": "PAM70", "title": "Predefined scoring matrices", "object": "PAM70", "file": "PAM70.rda", "class": [ "moved_to_pwalign_pkg", "matrix", "array" ], "fields": [ "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "J", "Z", "X", "*" ], "rows": 25, "table": true, "tojson": true }, { "name": "yeastSEQCHR1", "title": "An annotation data file for CHR1 in the yeastSEQ package", "object": "yeastSEQCHR1", "file": "yeastSEQCHR1.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "AAString-class", "title": "AAString objects", "topics": [ "AAString", "AAString-class", "AA_ALPHABET", "AA_PROTEINOGENIC", "AA_STANDARD", "class:AAString" ] }, { "page": "AMINO_ACID_CODE", "title": "The Single-Letter Amino Acid Code", "topics": [ "AMINO_ACID_CODE" ] }, { "page": "chartr", "title": "Replace letters in a sequence or set of sequences", "topics": [ "chartr", "chartr,ANY,ANY,MaskedXString-method", "chartr,ANY,ANY,XString-method", "chartr,ANY,ANY,XStringSet-method", "chartr,ANY,ANY,XStringViews-method", "replaceAmbiguities" ] }, { "page": "coloring", "title": "XString Display Colors", "topics": [ "coloring", "update_AA_palette", "update_B_palette", "update_DNA_palette", "update_RNA_palette", "update_X_palette" ] }, { "page": "dinucleotideFrequencyTest", "title": "Pearson's chi-squared Test and G-tests for String Position Dependence", "topics": [ "dinucleotideFrequencyTest", "dinucleotideFrequencyTest,DNAStringSet-method", "dinucleotideFrequencyTest,RNAStringSet-method" ] }, { "page": "DNAString-class", "title": "DNAString objects", "topics": [ "class:DNAString", "DNAString", "DNAString-class", "DNA_ALPHABET", "DNA_BASES" ] }, { "page": "findPalindromes", "title": "Searching a sequence for palindromes", "topics": [ "findPalindromes", "findPalindromes,DNAString-method", "findPalindromes,MaskedXString-method", "findPalindromes,RNAString-method", "findPalindromes,XString-method", "findPalindromes,XStringViews-method", "palindromeArmLength", "palindromeArmLength,DNAString-method", "palindromeArmLength,RNAString-method", "palindromeArmLength,XString-method", "palindromeArmLength,XStringSet-method", "palindromeArmLength,XStringViews-method", "palindromeLeftArm", "palindromeLeftArm,XString-method", "palindromeLeftArm,XStringViews-method", "palindromeRightArm", "palindromeRightArm,XString-method", "palindromeRightArm,XStringViews-method" ] }, { "page": "GENETIC_CODE", "title": "The Standard Genetic Code and its known variants", "topics": [ "GENETIC_CODE", "GENETIC_CODE_TABLE", "getGeneticCode", "RNA_GENETIC_CODE" ] }, { "page": "getSeq", "title": "getSeq", "topics": [ "getSeq" ] }, { "page": "gregexpr2", "title": "A replacement for R standard gregexpr function", "topics": [ "gregexpr2" ] }, { "page": "HNF4alpha", "title": "Known HNF4alpha binding sequences", "topics": [ "HNF4alpha" ] }, { "page": "injectHardMask", "title": "Injecting a hard mask in a sequence", "topics": [ "injectHardMask", "injectHardMask,MaskedXString-method", "injectHardMask,XStringViews-method" ] }, { "page": "IUPAC_CODE_MAP", "title": "The IUPAC Extended Genetic Alphabet", "topics": [ "IUPAC_CODE_MAP", "mergeIUPACLetters" ] }, { "page": "lcsuffix", "title": "Find Longest Common Prefix/Suffix", "topics": [ "lcprefix", "lcprefix,character,character-method", "lcprefix,character,XString-method", "lcprefix,XString,character-method", "lcprefix,XString,XString-method", "lcsuffix", "lcsuffix,character,character-method", "lcsuffix,character,XString-method", "lcsuffix,XString,character-method", "lcsuffix,XString,XString-method" ] }, { "page": "letter", "title": "Subsetting a string", "topics": [ "letter", "letter,character-method", "letter,MaskedXString-method", "letter,XString-method", "letter,XStringViews-method" ] }, { "page": "letterFrequency", "title": "Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences", "topics": [ "alphabetFrequency", "alphabetFrequency,AAString-method", "alphabetFrequency,AAStringSet-method", "alphabetFrequency,DNAString-method", "alphabetFrequency,DNAStringSet-method", "alphabetFrequency,MaskedXString-method", "alphabetFrequency,RNAString-method", "alphabetFrequency,RNAStringSet-method", "alphabetFrequency,XString-method", "alphabetFrequency,XStringSet-method", "alphabetFrequency,XStringViews-method", "consensusMatrix", "consensusMatrix,character-method", "consensusMatrix,matrix-method", "consensusMatrix,XStringSet-method", "consensusMatrix,XStringViews-method", "consensusString", "consensusString,ANY-method", "consensusString,BStringSet-method", "consensusString,DNAStringSet-method", "consensusString,matrix-method", "consensusString,RNAStringSet-method", "consensusString,XStringViews-method", "hasOnlyBaseLetters", "hasOnlyBaseLetters,DNAString-method", "hasOnlyBaseLetters,DNAStringSet-method", "hasOnlyBaseLetters,MaskedXString-method", "hasOnlyBaseLetters,RNAString-method", "hasOnlyBaseLetters,RNAStringSet-method", "hasOnlyBaseLetters,XStringViews-method", "letterFrequency", "letterFrequency,MaskedXString-method", "letterFrequency,XString-method", "letterFrequency,XStringSet-method", "letterFrequency,XStringViews-method", "letterFrequencyInSlidingView", "letterFrequencyInSlidingView,XString-method", "uniqueLetters", "uniqueLetters,MaskedXString-method", "uniqueLetters,XString-method", "uniqueLetters,XStringSet-method", "uniqueLetters,XStringViews-method" ] }, { "page": "longestConsecutive", "title": "Obtain the length of the longest substring containing only 'letter'", "topics": [ "longestConsecutive" ] }, { "page": "lowlevel-matching", "title": "Low-level matching functions", "topics": [ "hasLetterAt", "isMatchingAt", "isMatchingEndingAt", "isMatchingEndingAt,character-method", "isMatchingEndingAt,XString-method", "isMatchingEndingAt,XStringSet-method", "isMatchingStartingAt", "isMatchingStartingAt,character-method", "isMatchingStartingAt,XString-method", "isMatchingStartingAt,XStringSet-method", "lowlevel-matching", "neditAt", "neditEndingAt", "neditEndingAt,character-method", "neditEndingAt,XString-method", "neditEndingAt,XStringSet-method", "neditStartingAt", "neditStartingAt,character-method", "neditStartingAt,XString-method", "neditStartingAt,XStringSet-method", "which.isMatchingAt", "which.isMatchingEndingAt", "which.isMatchingEndingAt,character-method", "which.isMatchingEndingAt,XString-method", "which.isMatchingEndingAt,XStringSet-method", "which.isMatchingStartingAt", "which.isMatchingStartingAt,character-method", "which.isMatchingStartingAt,XString-method", "which.isMatchingStartingAt,XStringSet-method" ] }, { "page": "MaskedXString-class", "title": "MaskedXString objects", "topics": [ "as.character,MaskedXString-method", "class:MaskedAAString", "class:MaskedBString", "class:MaskedDNAString", "class:MaskedRNAString", "class:MaskedXString", "coerce,AAString,MaskedAAString-method", "coerce,BString,MaskedBString-method", "coerce,DNAString,MaskedDNAString-method", "coerce,MaskedAAString,AAString-method", "coerce,MaskedBString,BString-method", "coerce,MaskedDNAString,DNAString-method", "coerce,MaskedRNAString,RNAString-method", "coerce,MaskedXString,MaskCollection-method", "coerce,MaskedXString,MaskedAAString-method", "coerce,MaskedXString,MaskedBString-method", "coerce,MaskedXString,MaskedDNAString-method", "coerce,MaskedXString,MaskedRNAString-method", "coerce,MaskedXString,NormalIRanges-method", "coerce,MaskedXString,Views-method", "coerce,MaskedXString,XStringViews-method", "coerce,RNAString,MaskedRNAString-method", "collapse,MaskedXString-method", "gaps,MaskedXString-method", "length,MaskedXString-method", "MaskedAAString", "MaskedAAString-class", "MaskedBString", "MaskedBString-class", "MaskedDNAString", "MaskedDNAString-class", "maskedratio,MaskedXString-method", "MaskedRNAString", "MaskedRNAString-class", "maskedwidth,MaskedXString-method", "MaskedXString", "MaskedXString-class", "masks", "masks,MaskedXString-method", "masks,XString-method", "masks<-", "masks<-,MaskedXString,MaskCollection-method", "masks<-,MaskedXString,NULL-method", "masks<-,XString,ANY-method", "masks<-,XString,NULL-method", "nchar,MaskedXString-method", "seqtype,MaskedXString-method", "seqtype<-,MaskedXString-method", "show,MaskedXString-method", "subseq,MaskedXString-method", "toString,MaskedXString-method", "unmasked", "unmasked,MaskedXString-method", "unmasked,XString-method", "Views,MaskedXString-method" ] }, { "page": "maskMotif", "title": "Masking by content (or by position)", "topics": [ "mask", "maskMotif", "maskMotif,MaskedXString,character-method", "maskMotif,MaskedXString,XString-method", "maskMotif,XString,ANY-method" ] }, { "page": "match-utils", "title": "Utility functions operating on the matches returned by a high-level matching function", "topics": [ "coverage,MaskedXString-method", "coverage,MIndex-method", "match-utils", "mismatch", "mismatch,ANY,XStringViews-method", "nmatch", "nmatch,ANY,XStringViews-method", "nmismatch", "nmismatch,ANY,XStringViews-method" ] }, { "page": "matchLRPatterns", "title": "Find paired matches in a sequence", "topics": [ "matchLRPatterns", "matchLRPatterns,MaskedXString-method", "matchLRPatterns,XString-method", "matchLRPatterns,XStringViews-method" ] }, { "page": "matchPattern", "title": "String searching functions", "topics": [ "countPattern", "countPattern,character-method", "countPattern,MaskedXString-method", "countPattern,XString-method", "countPattern,XStringSet-method", "countPattern,XStringViews-method", "matchPattern", "matchPattern,character-method", "matchPattern,MaskedXString-method", "matchPattern,XString-method", "matchPattern,XStringSet-method", "matchPattern,XStringViews-method", "vcountPattern", "vcountPattern,character-method", "vcountPattern,MaskedXString-method", "vcountPattern,XString-method", "vcountPattern,XStringSet-method", "vcountPattern,XStringViews-method", "vmatchPattern", "vmatchPattern,character-method", "vmatchPattern,MaskedXString-method", "vmatchPattern,XString-method", "vmatchPattern,XStringSet-method", "vmatchPattern,XStringViews-method" ] }, { "page": "matchPDict-exact", "title": "Matching a dictionary of patterns against a reference", "topics": [ "countPDict", "countPDict,MaskedXString-method", "countPDict,XString-method", "countPDict,XStringSet-method", "countPDict,XStringViews-method", "extractAllMatches", "matchPDict", "matchPDict,MaskedXString-method", "matchPDict,XString-method", "matchPDict,XStringSet-method", "matchPDict,XStringViews-method", "matchPDict-exact", "vcountPDict", "vcountPDict,MaskedXString-method", "vcountPDict,XString-method", "vcountPDict,XStringSet-method", "vcountPDict,XStringViews-method", "vmatchPDict", "vmatchPDict,ANY-method", "vmatchPDict,MaskedXString-method", "vmatchPDict,XString-method", "vwhichPDict", "vwhichPDict,MaskedXString-method", "vwhichPDict,XString-method", "vwhichPDict,XStringSet-method", "vwhichPDict,XStringViews-method", "whichPDict", "whichPDict,MaskedXString-method", "whichPDict,XString-method", "whichPDict,XStringSet-method", "whichPDict,XStringViews-method" ] }, { "page": "matchPDict-inexact", "title": "Inexact matching with matchPDict()/countPDict()/whichPDict()", "topics": [ "matchPDict-inexact" ] }, { "page": "matchProbePair", "title": "Find \"theoretical amplicons\" mapped to a probe pair", "topics": [ "matchProbePair", "matchProbePair,DNAString-method", "matchProbePair,MaskedDNAString-method", "matchProbePair,XStringViews-method" ] }, { "page": "matchPWM", "title": "PWM creating, matching, and related utilities", "topics": [ "countPWM", "countPWM,character-method", "countPWM,DNAString-method", "countPWM,MaskedDNAString-method", "countPWM,XStringViews-method", "matchPWM", "matchPWM,character-method", "matchPWM,DNAString-method", "matchPWM,MaskedDNAString-method", "matchPWM,XStringViews-method", "maxScore", "maxScore,ANY-method", "maxWeights", "maxWeights,matrix-method", "minScore", "minScore,ANY-method", "minWeights", "minWeights,matrix-method", "PWM", "PWM,character-method", "PWM,DNAStringSet-method", "PWM,matrix-method", "PWMscoreStartingAt", "reverseComplement,matrix-method", "unitScale" ] }, { "page": "MIndex-class", "title": "MIndex objects", "topics": [ "ByPos_MIndex-class", "class:ByPos_MIndex", "class:MIndex", "coerce,MIndex,CompressedIRangesList-method", "elementNROWS,MIndex-method", "endIndex", "endIndex,ByPos_MIndex-method", "length,MIndex-method", "MIndex", "MIndex-class", "names,MIndex-method", "names<-,MIndex-method", "show,MIndex-method", "startIndex", "startIndex,ByPos_MIndex-method", "unlist,MIndex-method", "width0", "width0,MIndex-method", "[[,ByPos_MIndex-method" ] }, { "page": "MIndexList-class", "title": "MIndexList objects", "topics": [ "class:MIndexList", "coerce,List,MIndexList-method", "coerce,list,MIndexList-method", "MIndexList", "MIndexList-class", "show,MIndexList-method", "showAsCell,MIndexList-method" ] }, { "page": "misc", "title": "Some miscellaneous stuff", "topics": [ "misc", "N50" ] }, { "page": "MultipleAlignment-class", "title": "MultipleAlignment objects", "topics": [ "AAMultipleAlignment", "AAMultipleAlignment-class", "alphabetFrequency,MultipleAlignment-method", "as.character,MultipleAlignment-method", "as.matrix,MultipleAlignment-method", "class:AAMultipleAlignment", "class:DNAMultipleAlignment", "class:MultipleAlignment", "class:RNAMultipleAlignment", "coerce,character,AAMultipleAlignment-method", "coerce,character,DNAMultipleAlignment-method", "coerce,character,RNAMultipleAlignment-method", "coerce,MultipleAlignment,AAStringSet-method", "coerce,MultipleAlignment,BStringSet-method", "coerce,MultipleAlignment,DNAStringSet-method", "coerce,MultipleAlignment,RNAStringSet-method", "colmask", "colmask,MultipleAlignment-method", "colmask<-", "colmask<-,MultipleAlignment,ANY-method", "colmask<-,MultipleAlignment,NULL-method", "consensusMatrix,MultipleAlignment-method", "consensusString,AAMultipleAlignment-method", "consensusString,DNAMultipleAlignment-method", "consensusString,MultipleAlignment-method", "consensusString,RNAMultipleAlignment-method", "consensusViews", "consensusViews,AAMultipleAlignment-method", "consensusViews,DNAMultipleAlignment-method", "consensusViews,MultipleAlignment-method", "consensusViews,RNAMultipleAlignment-method", "detail,MultipleAlignment-method", "dim,MultipleAlignment-method", "DNAMultipleAlignment", "DNAMultipleAlignment-class", "maskeddim", "maskeddim,MultipleAlignment-method", "maskedncol", "maskedncol,MultipleAlignment-method", "maskednrow", "maskednrow,MultipleAlignment-method", "maskedratio,MultipleAlignment-method", "maskGaps", "maskGaps,MultipleAlignment-method", "maskMotif,MultipleAlignment,ANY-method", "MultipleAlignment", "MultipleAlignment-class", "nchar,MultipleAlignment-method", "ncol,MultipleAlignment-method", "nrow,MultipleAlignment-method", "readAAMultipleAlignment", "readDNAMultipleAlignment", "readRNAMultipleAlignment", "RNAMultipleAlignment", "RNAMultipleAlignment-class", "rowmask", "rowmask,MultipleAlignment-method", "rowmask<-", "rowmask<-,MultipleAlignment,ANY-method", "rowmask<-,MultipleAlignment,NULL-method", "rownames,MultipleAlignment-method", "rownames<-,MultipleAlignment-method", "seqtype,MultipleAlignment-method", "show,MultipleAlignment-method", "unmasked,MultipleAlignment-method", "write.phylip" ] }, { "page": "nucleotideFrequency", "title": "Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)", "topics": [ "dinucleotideFrequency", "mkAllStrings", "nucleotideFrequencyAt", "nucleotideFrequencyAt,XStringSet-method", "nucleotideFrequencyAt,XStringViews-method", "oligonucleotideFrequency", "oligonucleotideFrequency,MaskedXString-method", "oligonucleotideFrequency,XString-method", "oligonucleotideFrequency,XStringSet-method", "oligonucleotideFrequency,XStringViews-method", "oligonucleotideTransitions", "trinucleotideFrequency" ] }, { "page": "padAndClip", "title": "Pad and clip strings", "topics": [ "padAndClip", "stackStrings" ] }, { "page": "PDict-class", "title": "PDict objects", "topics": [ "ACtree2", "ACtree2-class", "as.list,MTB_PDict-method", "class:ACtree2", "class:Expanded_TB_PDict", "class:MTB_PDict", "class:PDict", "class:PDict3Parts", "class:PreprocessedTB", "class:TB_PDict", "class:Twobit", "computeAllFlinks", "computeAllFlinks,ACtree2-method", "duplicated,PDict-method", "duplicated,PreprocessedTB-method", "Expanded_TB_PDict", "Expanded_TB_PDict-class", "hasAllFlinks", "hasAllFlinks,ACtree2-method", "head,PDict3Parts-method", "head,TB_PDict-method", "initialize,ACtree2-method", "initialize,PreprocessedTB-method", "initialize,Twobit-method", "length,PDict-method", "length,PDict3Parts-method", "length,PreprocessedTB-method", "MTB_PDict", "MTB_PDict-class", "names,PDict-method", "names<-,PDict-method", "nnodes", "nnodes,ACtree2-method", "patternFrequency", "patternFrequency,PDict-method", "PDict", "PDict,AsIs-method", "PDict,character-method", "PDict,DNAStringSet-method", "PDict,probetable-method", "PDict,XStringViews-method", "PDict-class", "PDict3Parts", "PDict3Parts-class", "PreprocessedTB", "PreprocessedTB-class", "show,ACtree2-method", "show,MTB_PDict-method", "show,TB_PDict-method", "show,Twobit-method", "tail,PDict3Parts-method", "tail,TB_PDict-method", "tb", "tb,PDict3Parts-method", "tb,PreprocessedTB-method", "tb,TB_PDict-method", "tb.width", "tb.width,PDict3Parts-method", "tb.width,PreprocessedTB-method", "tb.width,TB_PDict-method", "TB_PDict", "TB_PDict-class", "Twobit", "Twobit-class", "width,PDict-method", "width,PDict3Parts-method", "width,PreprocessedTB-method", "[[,PDict-method" ] }, { "page": "predefined_scoring_matrices", "title": "Predefined scoring matrices", "topics": [ "BLOSUM100", "BLOSUM45", "BLOSUM50", "BLOSUM62", "BLOSUM80", "PAM120", "PAM250", "PAM30", "PAM40", "PAM70", "predefined_scoring_matrices", "print.moved_to_pwalign_pkg" ] }, { "page": "QualityScaledXStringSet-class", "title": "QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects", "topics": [ "class:QualityScaledAAStringSet", "class:QualityScaledBStringSet", "class:QualityScaledDNAStringSet", "class:QualityScaledRNAStringSet", "class:QualityScaledXStringSet", "narrow,QualityScaledXStringSet-method", "parallel_slot_names,QualityScaledXStringSet-method", "quality", "quality,QualityScaledXStringSet-method", "QualityScaledAAStringSet", "QualityScaledAAStringSet-class", "QualityScaledBStringSet", "QualityScaledBStringSet-class", "QualityScaledDNAStringSet", "QualityScaledDNAStringSet-class", "QualityScaledRNAStringSet", "QualityScaledRNAStringSet-class", "QualityScaledXStringSet", "QualityScaledXStringSet-class", "readQualityScaledDNAStringSet", "reverse,QualityScaledXStringSet-method", "reverseComplement,QualityScaledDNAStringSet-method", "reverseComplement,QualityScaledRNAStringSet-method", "show,QualityScaledXStringSet-method", "windows,QualityScaledXStringSet-method", "writeQualityScaledXStringSet" ] }, { "page": "replaceAt", "title": "Extract/replace arbitrary substrings from/in a string or set of strings.", "topics": [ "extractAt", "extractAt,XString-method", "extractAt,XStringSet-method", "replaceAt", "replaceAt,XString-method", "replaceAt,XStringSet-method" ] }, { "page": "replaceLetterAt", "title": "Replacing letters in a sequence (or set of sequences) at some specified locations", "topics": [ ".inplaceReplaceLetterAt", "replaceLetterAt", "replaceLetterAt,DNAString-method", "replaceLetterAt,DNAStringSet-method" ] }, { "page": "reverseComplement", "title": "Sequence reversing and complementing", "topics": [ "complement", "complement,DNAString-method", "complement,DNAStringSet-method", "complement,MaskedDNAString-method", "complement,MaskedRNAString-method", "complement,RNAString-method", "complement,RNAStringSet-method", "complement,XStringViews-method", "reverse,MaskedXString-method", "reverseComplement", "reverseComplement,DNAString-method", "reverseComplement,DNAStringSet-method", "reverseComplement,MaskedDNAString-method", "reverseComplement,MaskedRNAString-method", "reverseComplement,RNAString-method", "reverseComplement,RNAStringSet-method", "reverseComplement,XStringViews-method" ] }, { "page": "RNAString-class", "title": "RNAString objects", "topics": [ "class:RNAString", "RNAString", "RNAString-class", "RNA_ALPHABET", "RNA_BASES" ] }, { "page": "seqinfo-methods", "title": "seqinfo() method for DNAStringSet objects", "topics": [ "seqinfo", "seqinfo,DNAStringSet-method", "seqinfo<-,DNAStringSet-method" ] }, { "page": "toComplex", "title": "Turning a DNA sequence into a vector of complex numbers", "topics": [ "toComplex", "toComplex,DNAString-method" ] }, { "page": "translate", "title": "Translating DNA/RNA sequences", "topics": [ "codons", "codons,DNAString-method", "codons,MaskedDNAString-method", "codons,MaskedRNAString-method", "codons,RNAString-method", "translate", "translate,DNAString-method", "translate,DNAStringSet-method", "translate,MaskedDNAString-method", "translate,MaskedRNAString-method", "translate,RNAString-method", "translate,RNAStringSet-method" ] }, { "page": "trimLRPatterns", "title": "Trim Flanking Patterns from Sequences", "topics": [ "trimLRPatterns", "trimLRPatterns,character-method", "trimLRPatterns,XString-method", "trimLRPatterns,XStringSet-method" ] }, { "page": "xscat", "title": "Concatenate sequences contained in XString, XStringSet and/or XStringViews objects", "topics": [ "xscat" ] }, { "page": "XString-class", "title": "BString objects", "topics": [ "alphabet", "alphabet,ANY-method", "as.character,XString-method", "as.vector,XString-method", "BString", "BString-class", "class:BString", "class:XString", "coerce,character,AAString-method", "coerce,character,BString-method", "coerce,character,DNAString-method", "coerce,character,RNAString-method", "coerce,character,XString-method", "coerce,XString,AAString-method", "coerce,XString,BString-method", "coerce,XString,DNAString-method", "coerce,XString,RNAString-method", "Compare,character,XString-method", "Compare,XString,character-method", "Compare,XString,XString-method", "nchar,XString-method", "seqtype,AAString-method", "seqtype,BString-method", "seqtype,DNAString-method", "seqtype,RNAString-method", "seqtype<-,XString-method", "show,XString-method", "showAsCell,XString-method", "substr,XString-method", "substring,XString-method", "toString,XString-method", "updateObject,AAString-method", "updateObject,XString-method", "XString", "XString-class" ] }, { "page": "XStringQuality-class", "title": "PhredQuality, SolexaQuality and IlluminaQuality objects", "topics": [ "alphabet,XStringQuality-method", "as.matrix,XStringQuality-method", "as.vector,XStringQuality-method", "class:IlluminaQuality", "class:PhredQuality", "class:SolexaQuality", "class:XStringQuality", "coerce,BString,IlluminaQuality-method", "coerce,BString,PhredQuality-method", "coerce,BString,SolexaQuality-method", "coerce,BStringSet,IlluminaQuality-method", "coerce,BStringSet,PhredQuality-method", "coerce,BStringSet,SolexaQuality-method", "coerce,character,IlluminaQuality-method", "coerce,character,PhredQuality-method", "coerce,character,SolexaQuality-method", "coerce,integer,IlluminaQuality-method", "coerce,integer,PhredQuality-method", "coerce,integer,SolexaQuality-method", "coerce,IntegerList,IlluminaQuality-method", "coerce,IntegerList,PhredQuality-method", "coerce,IntegerList,SolexaQuality-method", "coerce,numeric,IlluminaQuality-method", "coerce,numeric,PhredQuality-method", "coerce,numeric,SolexaQuality-method", "coerce,NumericList,IlluminaQuality-method", "coerce,NumericList,PhredQuality-method", "coerce,NumericList,SolexaQuality-method", "coerce,XStringQuality,CompressedIntegerList-method", "coerce,XStringQuality,CompressedNumericList-method", "coerce,XStringQuality,IntegerList-method", "coerce,XStringQuality,matrix-method", "coerce,XStringQuality,NumericList-method", "encoding", "encoding,XStringQuality-method", "IlluminaQuality", "IlluminaQuality-class", "PhredQuality", "PhredQuality-class", "SolexaQuality", "SolexaQuality-class", "XStringQuality", "XStringQuality-class" ] }, { "page": "XStringSet-class", "title": "XStringSet objects", "topics": [ "AAStringSet", "AAStringSet-class", "anyNA,XStringSet-method", "as.character,XStringSet-method", "as.data.frame,XStringSet-method", "as.data.frame.XStringSet", "as.factor,XStringSet-method", "as.matrix,XStringSet-method", "as.vector,XStringSet-method", "BStringSet", "BStringSet-class", "class:AAStringSet", "class:BStringSet", "class:DNAStringSet", "class:RNAStringSet", "class:XStringSet", "coerce,ANY,AAStringSet-method", "coerce,ANY,BStringSet-method", "coerce,ANY,DNAStringSet-method", "coerce,ANY,RNAStringSet-method", "coerce,ANY,XStringSet-method", "DNAStringSet", "DNAStringSet-class", "is.na,XStringSet-method", "narrow,character-method", "nchar,XStringSet-method", "RNAStringSet", "RNAStringSet-class", "seqtype,XStringSet-method", "seqtype<-,XStringSet-method", "show,XStringSet-method", "showAsCell,XStringSet-method", "subseq,character-method", "subseq<-,character-method", "subseq<-,XStringSet-method", "threebands,character-method", "toString,XStringSet-method", "unlist,XStringSet-method", "updateObject,AAStringSet-method", "updateObject,XStringSet-method", "width,character-method", "windows,character-method", "XStringSet", "XStringSet-class" ] }, { "page": "XStringSet-comparison", "title": "Element-wise comparison of XStringSet objects", "topics": [ "match,Vector,XStringSet-method", "match,vector,XStringSet-method", "match,XStringSet,Vector-method", "match,XStringSet,vector-method", "match,XStringSet,XStringSet-method", "pcompare,Vector,XStringSet-method", "pcompare,vector,XStringSet-method", "pcompare,XStringSet,Vector-method", "pcompare,XStringSet,vector-method", "pcompare,XStringSet,XStringSet-method", "XStringSet-comparison" ] }, { "page": "XStringSet-io", "title": "Read/write an XStringSet object from/to a file", "topics": [ "fasta.index", "fasta.seqlengths", "fastq.geometry", "fastq.seqlengths", "readAAStringSet", "readBStringSet", "readDNAStringSet", "readRNAStringSet", "saveXStringSet", "writeXStringSet", "XStringSet-io" ] }, { "page": "XStringSetList-class", "title": "XStringSetList objects", "topics": [ "AAStringSetList", "AAStringSetList-class", "BStringSetList", "BStringSetList-class", "class:AAStringSetList", "class:BStringSetList", "class:DNAStringSetList", "class:RNAStringSetList", "class:XStringSetList", "coerce,List,AAStringSetList-method", "coerce,list,AAStringSetList-method", "coerce,List,BStringSetList-method", "coerce,list,BStringSetList-method", "coerce,List,DNAStringSetList-method", "coerce,list,DNAStringSetList-method", "coerce,List,RNAStringSetList-method", "coerce,list,RNAStringSetList-method", "coerce,List,XStringSetList-method", "coerce,list,XStringSetList-method", "DNAStringSetList", "DNAStringSetList-class", "nchar,XStringSetList-method", "relistToClass,XStringSet-method", "RNAStringSetList", "RNAStringSetList-class", "seqtype,XStringSetList-method", "seqtype<-,XStringSetList-method", "show,XStringSetList-method", "showAsCell,XStringSetList-method", "XStringSetList", "XStringSetList-class" ] }, { "page": "XStringViews-class", "title": "The XStringViews class", "topics": [ "!=,character,XStringViews-method", "!=,XString,XStringViews-method", "!=,XStringViews,character-method", "!=,XStringViews,XString-method", "!=,XStringViews,XStringViews-method", "==,character,XStringViews-method", "==,XString,XStringViews-method", "==,XStringViews,character-method", "==,XStringViews,XString-method", "==,XStringViews,XStringViews-method", "as.character,XStringViews-method", "as.data.frame,XStringViews-method", "as.data.frame.XStringViews", "as.matrix,XStringViews-method", "class:XStringViews", "coerce,XStringSet,Views-method", "coerce,XStringSet,XStringViews-method", "coerce,XStringViews,AAStringSet-method", "coerce,XStringViews,BStringSet-method", "coerce,XStringViews,DNAStringSet-method", "coerce,XStringViews,RNAStringSet-method", "coerce,XStringViews,XStringSet-method", "nchar,XStringViews-method", "seqtype,XStringViews-method", "seqtype<-,XStringViews-method", "show,XStringViews-method", "toString,XStringViews-method", "Views,character-method", "Views,XString-method", "XStringViews", "XStringViews-class" ] }, { "page": "yeastSEQCHR1", "title": "An annotation data file for CHR1 in the yeastSEQ package", "topics": [ "yeastSEQCHR1" ] } ], "_readme": "https://github.com/bioc/Biostrings/raw/HEAD/README.md", "_rundeps": [ "BiocGenerics", "crayon", "generics", "IRanges", "S4Vectors", "Seqinfo", "XVector" ], "_vignettes": [ { "source": "Biostrings2Classes.Rnw", "filename": "Biostrings2Classes.pdf", "title": "A short presentation of the basic classes defined in Biostrings 2", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 19:50:36", "modified": "2026-07-18 05:36:57", "commits": 2 }, { "source": "BiostringsQuickOverview.Rnw", "filename": "BiostringsQuickOverview.pdf", "title": "Biostrings Quick Overview", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 19:50:36", "modified": "2026-06-04 23:35:11", "commits": 7 }, { "source": "matchprobes.Rmd", "filename": "matchprobes.html", "title": "Using oligonucleotide microarray reporter sequence information for preprocessing and quality assessment", "author": "Wolfgang Huber, Robert Gentleman", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Using probe packages", "Basic functions", "Reverse and complementary sequence", "Matching sets of probes against each other", "Base content", "Relating to the features of an AffyBatch", "Some sequence related \"preprocessing and quality\" plots" ], "created": "2023-04-14 03:17:19", "modified": "2024-02-12 17:48:02", "commits": 2 }, { "source": "MultipleAlignments.Rmd", "filename": "MultipleAlignments.html", "title": "MultipleAlignment Objects", "engine": "knitr::rmarkdown", "headings": [], "created": "2024-06-07 17:02:07", "modified": "2026-06-04 23:35:11", "commits": 3 }, { "source": "PairwiseAlignments.Rnw", "filename": "PairwiseAlignments.pdf", "title": "Pairwise Sequence Alignments", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 19:50:36", "modified": "2024-04-23 05:10:42", "commits": 5 }, { "source": "SequenceMatching.Rmd", "filename": "SequenceMatching.html", "title": "Sequence Searching and Matching with Biostrings", "author": "Aidan Lakshman", "engine": "knitr::rmarkdown", "headings": [ "Brief Recap", "XString objects", "XStringSets", "XStringViews", "Summary", "Low-Level Matching", "Edit Distance", "Simple Matching", "Fixed Pattern Matching", "matchPattern", "countPattern", "One Pattern, Multiple Subjects", "Matching with PDicts", "What is a PDict?", "Exact Matching", "Trusted Bands", "Inexact Matching", "PDict Matching Without a PDict", "Performance Notes", "Other Matching Utilities", "Finding Mismatches", "Finding Coverage", "Biological Applications", "Finding Palindromes", "Finding Ampilicons for a Primer Pair", "Position Weight Matrix (PWM) Matching", "Further Reading", "Session info" ], "created": "2026-06-23 20:41:00", "modified": "2026-07-18 05:36:57", "commits": 2 } ], "_score": 18.419417797924087, "_indexed": true, "_nocasepkg": "biostrings", "_universes": [ "bioc", "hpages", "bioconductor" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.81.9", "date": "2026-11-01T12:57:17.000Z", "distro": "resolute", "arch": "aarch64", "commit": "fb0cd89830abd054cf2681d6bc6c929981e07b21", "fileid": "https://r2.ropensci.org/43c1554d4c50fc02f524b09ba6f32e17a197ee7845f004dea2685a3514ce09d1", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308102081" }, { "r": "4.7.0", "os": "linux", "version": "2.81.9", "date": "2026-11-01T12:58:51.000Z", "distro": "resolute", "arch": "x86_64", "commit": "fb0cd89830abd054cf2681d6bc6c929981e07b21", "fileid": "https://r2.ropensci.org/bcf8b7d72e33459f3b53055cff8904cd46c6f9ad79f613540eaa3a297202dca7", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308102081" }, { "r": "4.6.2", "os": "linux", "version": "2.81.9", "date": "2026-11-01T12:56:58.000Z", "distro": "resolute", "arch": "aarch64", "commit": "fb0cd89830abd054cf2681d6bc6c929981e07b21", "fileid": "https://r2.ropensci.org/01ba21abfa3f8e34ea821523889f1603b7b118f5e3bdf2651424961efa6eba61", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308102081" }, { "r": "4.6.2", "os": "linux", "version": "2.81.9", "date": "2026-11-01T12:59:27.000Z", "distro": "resolute", "arch": "x86_64", "commit": "fb0cd89830abd054cf2681d6bc6c929981e07b21", "fileid": "https://r2.ropensci.org/fddc7bad59f2bf1def9b721069fcfdba3586171f23a9b3af39ff629304209da8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308102081" }, { "r": "4.5.3", "os": "mac", "version": "2.81.9", "date": "2026-11-01T13:02:57.000Z", "arch": "aarch64", "commit": "fb0cd89830abd054cf2681d6bc6c929981e07b21", "fileid": "https://r2.ropensci.org/c57630d13f19ce6e5521de3ce94b1eea2ccf53e5b72b623b519c472da1ef11ae", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308102081" }, { "r": "4.5.3", "os": "mac", "version": "2.81.9", "date": "2026-11-01T13:03:21.000Z", "arch": "x86_64", "commit": "fb0cd89830abd054cf2681d6bc6c929981e07b21", "fileid": "https://r2.ropensci.org/a961ea61225845bf22a3e0faf523ea67be8874bf5a921b175281fa3dbcbec507", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308102081" }, { "r": "4.6.2", "os": "mac", "version": "2.81.9", "date": "2026-11-01T13:03:12.000Z", "arch": "aarch64", "commit": "fb0cd89830abd054cf2681d6bc6c929981e07b21", "fileid": "https://r2.ropensci.org/9a94985bb0c3aeabe2775731516941f3848ec0ac2c933c2f0f26cdabc31fca8d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308102081" }, { "r": "4.6.2", "os": "mac", "version": "2.81.9", "date": "2026-11-01T13:04:47.000Z", "arch": "x86_64", "commit": "fb0cd89830abd054cf2681d6bc6c929981e07b21", "fileid": "https://r2.ropensci.org/ee49eba9142736108271b7bf4d5ad18d9d15d0108eb2b9342ea99f5d31b72eae", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308102081" }, { "r": "4.6.0", "os": "wasm", "version": "2.81.9", "date": "2026-11-01T12:57:59.000Z", "arch": "emscripten", "commit": "fb0cd89830abd054cf2681d6bc6c929981e07b21", "fileid": "https://r2.ropensci.org/c9d36096c9f90bff3b8f62306afa7f777d1746167b8d435f29182c0371f5b33d", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308102081" }, { "r": "4.7.0", "os": "win", "version": "2.81.9", "date": "2026-11-01T12:58:18.000Z", "arch": "aarch64", "commit": "fb0cd89830abd054cf2681d6bc6c929981e07b21", "fileid": "https://r2.ropensci.org/a2a006515aab0975a6877539294e40cb3293f4d2dd9a04099c555c91a648ba1a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308102081" }, { "r": "4.7.0", "os": "win", "version": "2.81.9", "date": "2026-11-01T12:56:28.000Z", "arch": "x86_64", "commit": "fb0cd89830abd054cf2681d6bc6c929981e07b21", "fileid": "https://r2.ropensci.org/ac82ca6f48872d2275ed012ac565ad8cfceac713caeefd7139cfda772616a83e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308102081" }, { "r": "4.5.3", "os": "win", "version": "2.81.9", "date": "2026-11-01T12:56:44.000Z", "arch": "x86_64", "commit": "fb0cd89830abd054cf2681d6bc6c929981e07b21", "fileid": "https://r2.ropensci.org/d21b1a5a7e90a51d0f355917fe0fc72a9857fe124a2d750518b71ecb914a1fd7", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308102081" }, { "r": "4.6.2", "os": "win", "version": "2.81.9", "date": "2026-11-01T12:58:08.000Z", "arch": "aarch64", "commit": "fb0cd89830abd054cf2681d6bc6c929981e07b21", "fileid": "https://r2.ropensci.org/a5f12b8eeb60b3d8f957c4b1f4d6d37524548ab4734eccbb3fd29ebd77ddf7fb", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308102081" }, { "r": "4.6.2", "os": "win", "version": "2.81.9", "date": "2026-11-01T12:56:25.000Z", "arch": "x86_64", "commit": "fb0cd89830abd054cf2681d6bc6c929981e07b21", "fileid": "https://r2.ropensci.org/36586e0b9d6aba1aeb8d9563d99beff91a45da000de5b6778a0be0e737eaa880", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308102081" } ] }