{ "_id": "6aef202743b51afa49dd93f2", "Package": "VariantAnnotation", "Type": "Package", "Title": "Annotation of Genetic Variants", "Description": "Annotate variants, compute amino acid coding changes,\npredict coding outcomes.", "Version": "1.59.4", "Authors@R": "c(\nperson(\"Valerie\", \"Oberchain\", role=\"aut\"),\nperson(\"Martin\", \"Morgan\", role=\"aut\"),\nperson(\"Michael\", \"Lawrence\", role=\"aut\"),\nperson(\"Stephanie\", \"Gogarten\", role=\"ctb\"),\nperson(\"Bioconductor Package Maintainer\", role=\"cre\",\nemail=\"maintainer@bioconductor.org\"))", "License": "Artistic-2.0", "SystemRequirements": "GNU make", "LazyLoad": "yes", "biocViews": "DataImport, Sequencing, SNP, Annotation, Genetics,\nVariantAnnotation", "Video": "https://www.youtube.com/watch?v=Ro0lHQ_J--I&list=UUqaMSQd_h-2EDGsU6WDiX0Q", "RoxygenNote": "7.3.1", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-07-24 10:23:12 UTC", "RemoteUrl": "https://github.com/bioc/VariantAnnotation", "RemoteRef": "HEAD", "RemoteSha": "6ab3a56c164777962b309123ef993ae6b45c405c", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-11-07 12:29:03 UTC", "User": "root" }, "Author": "Valerie Oberchain [aut],\nMartin Morgan [aut],\nMichael Lawrence [aut],\nStephanie Gogarten [ctb],\nBioconductor Package Maintainer [cre]", "Maintainer": "Bioconductor Package Maintainer ", "_user": "bioc", "_type": "src", "_file": "VariantAnnotation_1.59.4.tar.gz", "_fileid": "https://r2.ropensci.org/31d025e07ad6f2035381a8e1851cf4d1ce47df6a47b42a0ac8186289bad8b3b4", "_filesize": 1673325, "_sha256": "31d025e07ad6f2035381a8e1851cf4d1ce47df6a47b42a0ac8186289bad8b3b4", "_expires": "2027-02-15T12:57:09.000Z", "_created": "2026-11-07T12:29:03.000Z", "_published": "2026-11-07T12:57:11.388Z", "_upstream": "https://github.com/bioc/VariantAnnotation", "_status": "failure", "_maintainer": { "name": "Bioconductor Package Maintainer", "email": "maintainer@bioconductor.org", "login": "bioconductor-bot", "description": "", "uuid": 11681645 }, "_jobs": [ { "job": 128404128028, "time": 414, "config": "bioc-checks", "r": "4.6.2", "check": "WARNING", "artifact": "13573824205" }, { "job": 128404128082, "time": 679, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "13574528942" }, { "job": 128404128063, "time": 979, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "13574798051" }, { "job": 128404128036, "time": 687, "config": "linux-release-arm64", "r": "4.6.2", "check": "ERROR", "artifact": "13574479173" }, { "job": 128404128031, "time": 941, "config": "linux-release-x86_64", "r": "4.6.2", "check": "ERROR", "artifact": "13575055288" }, { "job": 128404128091, "time": 919, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "13575360469" }, { "job": 128404128090, "time": 1329, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "13574588844" }, { "job": 128404128102, "time": 768, "config": "macos-release-arm64", "r": "4.6.2", "check": "ERROR", "artifact": "13573944291" }, { "job": 128404128060, "time": 1030, "config": "macos-release-x86_64", "r": "4.6.2", "check": "ERROR", "artifact": "13574633335" }, { "job": 128402107788, "time": 553, "config": "source", "r": "4.6.2", "check": "ERROR", "artifact": "13573957528" }, { "job": 128404127988, "time": 295, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13574463214" }, { "job": 128404128145, "time": 907, "config": "windows-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "13575275137" }, { "job": 128404128050, "time": 868, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "13574658968" }, { "job": 128404128113, "time": 906, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "13573944117" }, { "job": 128404128047, "time": 869, "config": "windows-release-arm64", "r": "4.6.2", "check": "ERROR", "artifact": "13574409543" }, { "job": 128404128043, "time": 917, "config": "windows-release-x86_64", "r": "4.6.2", "check": "ERROR", "artifact": "13574778248" } ], "_bioccheck": { "error": 0, "warning": 4, "note": 19 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/42372061105", "_commit": { "id": "6ab3a56c164777962b309123ef993ae6b45c405c", "author": "vjcitn ", "committer": "vjcitn ", "message": "bump version for pr 74\n", "time": 1784888592 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "BiocGenerics", "version": ">= 0.37.0", "role": "Depends" }, { "package": "MatrixGenerics", "role": "Depends" }, { "package": "Seqinfo", "role": "Depends" }, { "package": "GenomicRanges", "version": ">= 1.61.1", "role": "Depends" }, { "package": "SummarizedExperiment", "version": ">= 1.39.1", "role": "Depends" }, { "package": "Rsamtools", "version": ">= 2.25.1", "role": "Depends" }, { "package": "S4Vectors", "role": "LinkingTo" }, { "package": "IRanges", "role": "LinkingTo" }, { "package": "XVector", "role": "LinkingTo" }, { "package": "Biostrings", "role": "LinkingTo" }, { "package": "Rhtslib", "version": ">= 2.99.0", "role": "LinkingTo" }, { "package": "utils", "role": "Imports" }, { "package": "DBI", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "S4Vectors", "version": ">= 0.27.12", "role": "Imports" }, { "package": "IRanges", "version": ">= 2.23.9", "role": "Imports" }, { "package": "XVector", "version": ">= 0.29.2", "role": "Imports" }, { "package": "Biostrings", "version": ">= 2.77.2", "role": "Imports" }, { "package": "AnnotationDbi", "version": ">= 1.27.9", "role": "Imports" }, { "package": "rtracklayer", "version": ">= 1.69.1", "role": "Imports" }, { "package": "BSgenome", "version": ">= 1.77.1", "role": "Imports" }, { "package": "GenomicFeatures", "version": ">= 1.61.4", "role": "Imports" }, { "package": "curl", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "AnnotationHub", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg19", "role": "Suggests" }, { "package": "TxDb.Hsapiens.UCSC.hg19.knownGene", "role": "Suggests" }, { "package": "SNPlocs.Hsapiens.dbSNP144.GRCh37", "role": "Suggests" }, { "package": "SIFT.Hsapiens.dbSNP132", "role": "Suggests" }, { "package": "SIFT.Hsapiens.dbSNP137", "role": "Suggests" }, { "package": "PolyPhen.Hsapiens.dbSNP131", "role": "Suggests" }, { "package": "snpStats", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "magick", "role": "Suggests" }, { "package": "jsonlite", "role": "Suggests" }, { "package": "httr", "role": "Suggests" }, { "package": "rjsoncons", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 165, "_updates": [ { "week": "2025-51", "n": 3 }, { "week": "2026-18", "n": 2 }, { "week": "2026-29", "n": 2 }, { "week": "2026-30", "n": 4 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.59.4", "bioc": "3.24", "repository": "bioc", "r": "4.6.0" }, { "branch": "release", "version": "1.58.0", "bioc": "3.23", "repository": "bioc", "r": "4.6.0" } ], "_topics": [ "dataimport", "sequencing", "snp", "annotation", "genetics", "variantannotation", "curl", "bzip2", "xz-utils", "zlib" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 485, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 18780, "source": "https://www.bioconductor.org/packages/stats/bioc/VariantAnnotation" }, "_mentions": 47, "_searchresults": 2652, "_abi": { "exports": [ { "key": "VariantAnnotation::AllVariants", "hash": "b1988f4689f30cf7" }, { "key": "VariantAnnotation::CodingVariants", "hash": "f59a71ee3890cd0b" }, { "key": "VariantAnnotation::CollapsedVCF", "hash": "cf4ff8aca7daa652" }, { "key": "VariantAnnotation::CompressedVRangesList", "hash": "6105d919be1d07c0" }, { "key": "VariantAnnotation::ExpandedVCF", "hash": "9efb667b338caefa" }, { "key": "VariantAnnotation::FiveUTRVariants", "hash": "65a7e27849aed8a9" }, { "key": "VariantAnnotation::IntergenicVariants", "hash": "fd636012690b3f2d" }, { "key": "VariantAnnotation::IntronVariants", "hash": "3304169f32049eb5" }, { "key": "VariantAnnotation::PROVEANDb", "hash": "b828c41cd117da1b" }, { "key": "VariantAnnotation::PolyPhenDb", "hash": "652e66d80980bc9e" }, { "key": "VariantAnnotation::PromoterVariants", "hash": "e96eb88e4226b942" }, { "key": "VariantAnnotation::SIFTDb", "hash": "5b8ea15842b1d55b" }, { "key": "VariantAnnotation::ScanVcfParam", "hash": "95bae2bccaed5b4c" }, { "key": "VariantAnnotation::SimpleVRangesList", "hash": "a272ff9bcf6cc092" }, { "key": "VariantAnnotation::SpliceSiteVariants", "hash": "3fe1fa93201d7289" }, { "key": "VariantAnnotation::ThreeUTRVariants", "hash": "04906271ac953b6b" }, { "key": "VariantAnnotation::VCF", "hash": "4cebc0a55ea6bc27" }, { "key": "VariantAnnotation::VCFHeader", "hash": "9044388527cfc985" }, { "key": "VariantAnnotation::VRanges", "hash": "d1ae4c17d8761e54" }, { "key": "VariantAnnotation::VRangesList", "hash": "2f1be572a4d3f8ad" }, { "key": "VariantAnnotation::VariantType", "hash": "962524654da9978a" }, { "key": "VariantAnnotation::VcfFile", "hash": "91b4943fb2ce34ba" }, { "key": "VariantAnnotation::VcfFileList", "hash": "e3ca04c2b25eba20" }, { "key": "VariantAnnotation::characterOrRle", "hash": "86f8a07c7944b868" }, { "key": "VariantAnnotation::characterRle", "hash": "1e899b1c69451915" }, { "key": "VariantAnnotation::complexRle", "hash": "8e4676bf8dd53a9e" }, { "key": "VariantAnnotation::factorOrRle", "hash": "f6f6da9d45bfe96c" }, { "key": "VariantAnnotation::factorRle", "hash": "04fd409520645dd1" }, { "key": "VariantAnnotation::generic:ScanVcfParam", "hash": "c5364710f3194b79" }, { "key": "VariantAnnotation::generic:alt", "hash": "5f51df3cd58e5567" }, { "key": "VariantAnnotation::generic:alt<-", "hash": "e083a8fdbd4bc21c" }, { "key": "VariantAnnotation::generic:altDepth", "hash": "5da61e4207152530" }, { "key": "VariantAnnotation::generic:altFraction", "hash": "68c6d4ff2f2ee322" }, { "key": "VariantAnnotation::generic:asVCF", "hash": "8b367050e2e69225" }, { "key": "VariantAnnotation::generic:called", "hash": "c7590b86eb9a7af9" }, { "key": "VariantAnnotation::generic:contig", "hash": "e9c1a6cd661def1b" }, { "key": "VariantAnnotation::generic:downstream", "hash": "34ce4dbbce64f704" }, { "key": "VariantAnnotation::generic:downstream<-", "hash": "c806e4db9e816f9b" }, { "key": "VariantAnnotation::generic:filt", "hash": "45251fc1516bb38f" }, { "key": "VariantAnnotation::generic:filt<-", "hash": "88cc827783bcbb2e" }, { "key": "VariantAnnotation::generic:filterVcf", "hash": "54670a574ea71dbc" }, { "key": "VariantAnnotation::generic:fixed", "hash": "a3f790bb2bdd4cff" }, { "key": "VariantAnnotation::generic:fixed<-", "hash": "2f972496167c6e5b" }, { "key": "VariantAnnotation::generic:geno", "hash": "63d9cfffcf829353" }, { "key": "VariantAnnotation::generic:geno<-", "hash": "9a61e17d84090e34" }, { "key": "VariantAnnotation::generic:genotypeToSnpMatrix", "hash": "4d7cd0c7d04c0b52" }, { "key": "VariantAnnotation::generic:getTranscriptSeqs", "hash": "9fb0f66ae46d07ce" }, { "key": "VariantAnnotation::generic:hardFilters", "hash": "d808b5219103a528" }, { "key": "VariantAnnotation::generic:hardFilters<-", "hash": "bc9c1e4a60ad3826" }, { "key": "VariantAnnotation::generic:header", "hash": "eddea1dbab877c6e" }, { "key": "VariantAnnotation::generic:header<-", "hash": "9aea4a6400702f30" }, { "key": "VariantAnnotation::generic:idType", "hash": "d700fe5eb86e4612" }, { "key": "VariantAnnotation::generic:idType<-", "hash": "bae0028ed4d015ba" }, { "key": "VariantAnnotation::generic:indexVcf", "hash": "d0ecf54c990ca3b9" }, { "key": "VariantAnnotation::generic:info", "hash": "c17978b68b9bfa8d" }, { "key": "VariantAnnotation::generic:info<-", "hash": "16d7cd43c694d1ca" }, { "key": "VariantAnnotation::generic:intergenic", "hash": "f156dccb1af1ef31" }, { "key": "VariantAnnotation::generic:intergenic<-", "hash": "8c960b59a9c1eda2" }, { "key": "VariantAnnotation::generic:isDeletion", "hash": "f6863ceed3a64b5a" }, { "key": "VariantAnnotation::generic:isDelins", "hash": "e1388ae95511dd5f" }, { "key": "VariantAnnotation::generic:isIndel", "hash": "a7233192795c0ef5" }, { "key": "VariantAnnotation::generic:isInsertion", "hash": "a55da7ce5d73e0ea" }, { "key": "VariantAnnotation::generic:isSNV", "hash": "f9a7ca535a45d15b" }, { "key": "VariantAnnotation::generic:isSV", "hash": "5f0a0ff10f484c60" }, { "key": "VariantAnnotation::generic:isSVPrecise", "hash": "d7bc0487bd6c553e" }, { "key": "VariantAnnotation::generic:isSubstitution", "hash": "3a043922561f7415" }, { "key": "VariantAnnotation::generic:isTransition", "hash": "f391cd561455d598" }, { "key": "VariantAnnotation::generic:locateVariants", "hash": "c4721d8b8d39d922" }, { "key": "VariantAnnotation::generic:meta", "hash": "68e2ce96806031cd" }, { "key": "VariantAnnotation::generic:meta<-", "hash": "9b3107b3236b9234" }, { "key": "VariantAnnotation::generic:predictCoding", "hash": "7b6a3c067f7c7fa0" }, { "key": "VariantAnnotation::generic:promoter", "hash": "21d1ab0b1dd15e74" }, { "key": "VariantAnnotation::generic:promoter<-", "hash": "57e4273bef6206d5" }, { "key": "VariantAnnotation::generic:qual", "hash": "8160d5f84c4117a7" }, { "key": "VariantAnnotation::generic:qual<-", "hash": "6602d835c4ea3dec" }, { "key": "VariantAnnotation::generic:readVcf", "hash": "8ac10d783bb95fc7" }, { "key": "VariantAnnotation::generic:ref", "hash": "8b51cab1b9d3b2f1" }, { "key": "VariantAnnotation::generic:ref<-", "hash": "98f32a28c06420c1" }, { "key": "VariantAnnotation::generic:refDepth", "hash": "727a4fb07061d8e3" }, { "key": "VariantAnnotation::generic:refFraction", "hash": "13be340305b204a5" }, { "key": "VariantAnnotation::generic:reference", "hash": "bad0daa2760fe64e" }, { "key": "VariantAnnotation::generic:scanVcf", "hash": "e1ef9c082f120e5b" }, { "key": "VariantAnnotation::generic:scanVcfHeader", "hash": "01cb23f246618ac8" }, { "key": "VariantAnnotation::generic:snpSummary", "hash": "c892b88838d4c145" }, { "key": "VariantAnnotation::generic:softFilterMatrix", "hash": "979554c2be70a529" }, { "key": "VariantAnnotation::generic:softFilterMatrix<-", "hash": "85bf8911b4795126" }, { "key": "VariantAnnotation::generic:stackSamples", "hash": "698a3d62b08d5301" }, { "key": "VariantAnnotation::generic:summarizeVariants", "hash": "211f5b9498799a56" }, { "key": "VariantAnnotation::generic:tabulate", "hash": "9f14b34b3cf6fcec" }, { "key": "VariantAnnotation::generic:totalDepth", "hash": "8542e5ba62353c09" }, { "key": "VariantAnnotation::generic:upstream", "hash": "cf7f51096a880d89" }, { "key": "VariantAnnotation::generic:upstream<-", "hash": "601059511b6120ef" }, { "key": "VariantAnnotation::generic:vcfFields", "hash": "d95e32873dadc045" }, { "key": "VariantAnnotation::generic:writeVcf", "hash": "5b89edf8b09297fb" }, { "key": "VariantAnnotation::integerOrRle", "hash": "a243d6df3cb5744e" }, { "key": "VariantAnnotation::integerRle", "hash": "60d3b57b0040f1d4" }, { "key": "VariantAnnotation::logicalRle", "hash": "e3841f6de2ff352d" }, { "key": "VariantAnnotation::numericRle", "hash": "75f41339b178c56e" }, { "key": "VariantAnnotation::rawRle", "hash": "f015e367956814a4" } ], "imports": [ { "key": "AnnotationDbi::AnnotationDb", "hash": "a4bdd04b3ae79fb2" }, { "key": "AnnotationDbi::generic:columns", "hash": "05e2c7067b5e829f" }, { "key": "AnnotationDbi::generic:keys", "hash": "931ea12e0913cf48" }, { "key": "AnnotationDbi::generic:keytypes", "hash": "1861f8e46f59b1c3" }, { "key": "AnnotationDbi::generic:select", "hash": "ba90536ae2ef92ed" }, { "key": "BSgenome::GRanges_OR_NULL", "hash": "115e13d341b6edf1" }, { "key": "Biobase::generic:sampleNames", "hash": "a2de801cf7c1f59b" }, { "key": "Biobase::generic:sampleNames<-", "hash": "d5873cdad308bc75" }, { "key": "Biobase::generic:samples", "hash": "d02de789d4ab0ffa" }, { "key": "BiocGenerics::generic:cbind", "hash": "24fd9eb44785137b" }, { "key": "BiocGenerics::generic:duplicated", "hash": "677d6f0c28ec6b85" }, { "key": "BiocGenerics::generic:match", "hash": "d6f656cbb258bc6c" }, { "key": "BiocGenerics::generic:rbind", "hash": "f0a899e378313bb5" }, { "key": "BiocGenerics::generic:strand", "hash": "d8365ae61d4c6a88" }, { "key": "BiocGenerics::generic:strand<-", "hash": "7352eb7a11ab981d" }, { "key": "BiocGenerics::generic:updateObject", "hash": "2ce9a5b3171bccbf" }, { "key": "BiocIO::generic:import", "hash": "95a7d5ffdb2b9e00" }, { "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": "GenomicRanges::CompressedGRangesList", "hash": "58605f3dd28fdc9e" }, { "key": "GenomicRanges::CompressedGenomicRangesList", "hash": "776ab3ef3d88d432" }, { "key": "GenomicRanges::GRanges", "hash": "2f9f8bafb276e9ba" }, { "key": "GenomicRanges::GRangesList", "hash": "753c1390c911b00d" }, { "key": "GenomicRanges::GenomicRanges", "hash": "d3fda1b8c44bfd98" }, { "key": "GenomicRanges::GenomicRangesList", "hash": "087f0be08bea47f1" }, { "key": "GenomicRanges::GenomicRanges_OR_GRangesList", "hash": "d41eb908f2d4f222" }, { "key": "GenomicRanges::GenomicRanges_OR_GenomicRangesList", "hash": "ce9b8e58ffbeee53" }, { "key": "GenomicRanges::GenomicRanges_OR_missing", "hash": "c442ea820978b20d" }, { "key": "GenomicRanges::SimpleGRangesList", "hash": "89a3ca7b1d22fdb1" }, { "key": "GenomicRanges::SimpleGenomicRangesList", "hash": "de0b2ebe1bc327cf" }, { "key": "GenomicRanges::generic:extraColumnSlotNames", "hash": "437ecdd68326ce48" }, { "key": "IRanges::CompressedList", "hash": "b347e8e7407257ee" }, { "key": "IRanges::CompressedRangesList", "hash": "171e0bd5b0e240db" }, { "key": "IRanges::Ranges", "hash": "2ec1451ebae33ae7" }, { "key": "IRanges::RangesList", "hash": "0dc12cc95af5ec4b" }, { "key": "IRanges::SimpleRangesList", "hash": "9ae7e716b7d4e60f" }, { "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": "MatrixGenerics::generic:rowRanges", "hash": "0a235cbca5f40190" }, { "key": "Rsamtools::RsamtoolsFile", "hash": "d1d253aa6a234bf2" }, { "key": "Rsamtools::RsamtoolsFileList", "hash": "3e027c32f9826c96" }, { "key": "Rsamtools::ScanBVcfParam", "hash": "572d343b481ab44d" }, { "key": "Rsamtools::TabixFile", "hash": "ca137a938d807f71" }, { "key": "Rsamtools::TabixFileList", "hash": "0a1817ebf43cdfe5" }, { "key": "S4Vectors::Annotated", "hash": "9b5b8ee6ad9969f8" }, { "key": "S4Vectors::List", "hash": "90a253151dc8db9b" }, { "key": "S4Vectors::RectangularData", "hash": "d414a10823a4aada" }, { "key": "S4Vectors::Rle", "hash": "42d206ed89622f1e" }, { "key": "S4Vectors::SimpleList", "hash": "5a0b47349341c027" }, { "key": "S4Vectors::Vector", "hash": "09cab0bd77ae353b" }, { "key": "S4Vectors::generic:expand", "hash": "4edbdf73b7f30868" }, { "key": "S4Vectors::generic:mcols<-", "hash": "50480fd727ceae22" }, { "key": "S4Vectors::generic:parallel_slot_names", "hash": "7aa17c47f005eef5" }, { "key": "S4Vectors::generic:relistToClass", "hash": "5c47e2ea0d77491c" }, { "key": "S4Vectors::generic:replaceROWS", "hash": "a40feea23c8faf1e" }, { "key": "S4Vectors::generic:subsetByFilter", "hash": "968b6910139bace4" }, { "key": "S4Vectors::list_OR_List", "hash": "fcd6e1f6a8d39f9c" }, { "key": "S4Vectors::vector_OR_Vector", "hash": "f3fc18c9f8ff2633" }, { "key": "Seqinfo::generic:seqinfo", "hash": "1eb5bbe2fff73b75" }, { "key": "SummarizedExperiment::RangedSummarizedExperiment", "hash": "f15c4460724886cc" }, { "key": "SummarizedExperiment::SummarizedExperiment", "hash": "d53ca73257d1e8cf" }, { "key": "SummarizedExperiment::generic:rowRanges<-", "hash": "1793494cc48e7d16" }, { "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": "rtracklayer::generic:liftOver", "hash": "e1468736c46a0b55" } ] }, "_rbuild": "4.6.2", "_assets": [ "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/VariantAnnotation.html" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "AllVariants", "alt", "alt<-", "altDepth", "altDepth<-", "altFraction", "asVCF", "called", "cbind", "CodingVariants", "columns", "downstream", "downstream<-", "duplicateRSID", "expand", "filt", "filt<-", "filterVcf", "FiveUTRVariants", "fixed", "fixed<-", "geno", "geno<-", "genome", "genotypeCodesToNucleotides", "genotypeToSnpMatrix", "getSeq", "getTranscriptSeqs", "GLtoGP", "hardFilters", "hardFilters<-", "header", "header<-", "idType", "idType<-", "import", "indexVcf", "info", "info<-", "intergenic", "intergenic<-", "IntergenicVariants", "IntronVariants", "isDeletion", "isDelins", "isIndel", "isInsertion", "isSNV", "isSubstitution", "isTransition", "keys", "keytypes", "locateVariants", "makeVRangesFromGRanges", "mcols<-", "meta", "meta<-", "PLtoGP", "post_Hs_region", "predictCoding", "probabilityToSnpMatrix", "promoter", "promoter<-", "PromoterVariants", "qual", "qual<-", "rbind", "readGeno", "readGT", "readInfo", "readVcf", "readVcfAsVRanges", "ref", "ref<-", "refDepth", "refDepth<-", "reference", "resetFilter", "sampleNames", "sampleNames<-", "samples", "scanVcf", "scanVcfHeader", "ScanVcfParam", "select", "seqinfo", "seqlevels", "snpSummary", "softFilter", "softFilterMatrix", "softFilterMatrix<-", "SpliceSiteVariants", "stackSamples", "strand", "strand<-", "subset", "summarizeVariants", "tabulate", "ThreeUTRVariants", "totalDepth", "totalDepth<-", "updateObject", "upstream", "upstream<-", "VCF", "vcfFields", "VcfFile", "VcfFileList", "vcfFixed", "vcfFixed<-", "vcfGeno", "vcfGeno<-", "VCFHeader", "vcfInfo", "vcfInfo<-", "vcfSamples", "vcfSamples<-", "vcfTrimEmpty", "vcfTrimEmpty<-", "vcfWhich", "vcfWhich<-", "vep_by_region", "VRanges", "VRangesList", "VRangesScanVcfParam", "writeVcf" ], "_help": [ { "page": "filterVcf-methods", "title": "Filter VCF files", "topics": [ "filterVcf", "filterVcf,character-method", "filterVcf,TabixFile-method" ] }, { "page": "genotypeToSnpMatrix-methods", "title": "Convert genotype calls from a VCF file to a SnpMatrix object", "topics": [ "genotypeToSnpMatrix", "genotypeToSnpMatrix,array-method", "genotypeToSnpMatrix,CollapsedVCF-method" ] }, { "page": "getTranscriptSeqs-methods", "title": "Get transcript sequences", "topics": [ "getTranscriptSeqs", "getTranscriptSeqs,GRanges,FaFile-method", "getTranscriptSeqs,GRangesList,ANY-method", "getTranscriptSeqs,GRangesList,BSgenome-method", "getTranscriptSeqs,GRangesList,FaFile-method" ] }, { "page": "GLtoGP", "title": "Convert genotype likelihoods to genotype probabilities", "topics": [ "GLtoGP", "PLtoGP" ] }, { "page": "indexVcf-method", "title": "Create index files for VCF files", "topics": [ "indexVcf", "indexVcf,character-method", "indexVcf,VcfFile-method", "indexVcf,VcfFileList-method" ] }, { "page": "isSNV-methods", "title": "Identification of genomic variant types.", "topics": [ "isDeletion", "isDeletion,CollapsedVCF-method", "isDeletion,ExpandedVCF-method", "isDeletion,VRanges-method", "isDelins", "isDelins,CollapsedVCF-method", "isDelins,ExpandedVCF-method", "isDelins,VRanges-method", "isIndel", "isIndel,CollapsedVCF-method", "isIndel,ExpandedVCF-method", "isIndel,VRanges-method", "isInsertion", "isInsertion,CollapsedVCF-method", "isInsertion,ExpandedVCF-method", "isInsertion,VRanges-method", "isSNV", "isSNV,CollapsedVCF-method", "isSNV,ExpandedVCF-method", "isSNV,VRanges-method", "isSubstitution", "isSubstitution,CollapsedVCF-method", "isSubstitution,ExpandedVCF-method", "isSubstitution,VRanges-method", "isTransition", "isTransition,CollapsedVCF-method", "isTransition,ExpandedVCF-method", "isTransition,VRanges-method" ] }, { "page": "locateVariants-methods", "title": "Locate variants", "topics": [ "locateVariants", "locateVariants,GRanges,GRangesList,AllVariants-method", "locateVariants,GRanges,GRangesList,CodingVariants-method", "locateVariants,GRanges,GRangesList,FiveUTRVariants-method", "locateVariants,GRanges,GRangesList,IntergenicVariants-method", "locateVariants,GRanges,GRangesList,IntronVariants-method", "locateVariants,GRanges,GRangesList,PromoterVariants-method", "locateVariants,GRanges,GRangesList,SpliceSiteVariants-method", "locateVariants,GRanges,GRangesList,ThreeUTRVariants-method", "locateVariants,GRanges,GRangesList,VariantType-method", "locateVariants,GRanges,TxDb,AllVariants-method", "locateVariants,GRanges,TxDb,CodingVariants-method", "locateVariants,GRanges,TxDb,FiveUTRVariants-method", "locateVariants,GRanges,TxDb,IntergenicVariants-method", "locateVariants,GRanges,TxDb,IntronVariants-method", "locateVariants,GRanges,TxDb,PromoterVariants-method", "locateVariants,GRanges,TxDb,SpliceSiteVariants-method", "locateVariants,GRanges,TxDb,ThreeUTRVariants-method", "locateVariants,GRanges,TxDb,VariantType-method", "locateVariants,IntegerRanges,GRangesList,VariantType-method", "locateVariants,IntegerRanges,TxDb,VariantType-method", "locateVariants,VCF,GRangesList,VariantType-method", "locateVariants,VCF,TxDb,VariantType-method" ] }, { "page": "PolyPhenDb-class", "title": "PolyPhenDb objects", "topics": [ "class:PolyPhenDb", "columns,PolyPhenDb-method", "duplicateRSID", "keys,PolyPhenDb-method", "metadata,PolyPhenDb-method", "PolyPhen", "PolyPhenDb", "PolyPhenDb-class", "select,PolyPhenDb-method" ] }, { "page": "PolyPhenDbColumns", "title": "PolyPhenDb Columns", "topics": [ "PolyPhenDbColumns" ] }, { "page": "post_Hs_region", "title": "elementary vep/homo_sapiens/region call to ensembl VEP REST API", "topics": [ "post_Hs_region" ] }, { "page": "predictCoding-methods", "title": "Predict amino acid coding changes for variants", "topics": [ "predictCoding", "predictCoding,CollapsedVCF,TxDb,ANY,missing-method", "predictCoding,ExpandedVCF,TxDb,ANY,missing-method", "predictCoding,GRanges,TxDb,ANY,DNAStringSet-method", "predictCoding,IntegerRanges,TxDb,ANY,DNAStringSet-method", "predictCoding,VRanges,TxDb,ANY,missing-method" ] }, { "page": "probabilityToSnpMatrix", "title": "Convert posterior genotype probability to a SnpMatrix object", "topics": [ "probabilityToSnpMatrix" ] }, { "page": "PROVEANDb-class", "title": "PROVEANDb objects", "topics": [ "class:PROVEANDb", "columns,PROVEANDb-method", "keys,PROVEANDb-method", "keytypes,PROVEANDb-method", "PROVEAN", "PROVEANDb", "PROVEANDb-class", "select,PROVEANDb-method" ] }, { "page": "readVcf-methods", "title": "Read VCF files", "topics": [ "import,VcfFile,ANY,ANY-method", "readGeno", "readGT", "readInfo", "readVcf", "readVcf,character,ANY-method", "readVcf,character,missing-method", "readVcf,TabixFile,GRanges-method", "readVcf,TabixFile,GRangesList-method", "readVcf,TabixFile,IntegerRangesList-method", "readVcf,TabixFile,missing-method", "readVcf,TabixFile,ScanVcfParam-method" ] }, { "page": "scanVcf-methods", "title": "Import VCF files", "topics": [ "scanVcf", "scanVcf,character,missing-method", "scanVcf,character,ScanVcfParam-method", "scanVcf,connection,missing-method", "scanVcf,TabixFile,GRanges-method", "scanVcf,TabixFile,IntegerRangesList-method", "scanVcf,TabixFile,missing-method", "scanVcf,TabixFile,ScanVcfParam-method", "scanVcfHeader", "scanVcfHeader,character-method", "scanVcfHeader,missing-method", "scanVcfHeader,TabixFile-method" ] }, { "page": "ScanVcfParam-class", "title": "Parameters for scanning VCF files", "topics": [ "ScanVcfParam", "ScanVcfParam,ANY-method", "ScanVcfParam,missing-method", "ScanVcfParam-class", "vcfFixed", "vcfFixed<-", "vcfGeno", "vcfGeno<-", "vcfInfo", "vcfInfo<-", "vcfSamples", "vcfSamples<-", "vcfTrimEmpty", "vcfTrimEmpty<-", "vcfWhich", "vcfWhich<-" ] }, { "page": "seqinfo-method", "title": "Get seqinfo for VCF file", "topics": [ "seqinfo", "seqinfo,VcfFile-method", "seqinfo,VcfFileList-method" ] }, { "page": "SIFTDb-class", "title": "SIFTDb objects", "topics": [ "class:SIFTDb", "columns,SIFTDb-method", "keys,SIFTDb-method", "metadata,SIFTDb-method", "select,SIFTDb-method", "SIFT", "SIFTDb", "SIFTDb-class" ] }, { "page": "SIFTDbColumns", "title": "SIFTDb Columns", "topics": [ "SIFTDbColumns" ] }, { "page": "snpSummary", "title": "Counts and distribution statistics for SNPs in a VCF object", "topics": [ "snpSummary", "snpSummary,CollapsedVCF-method" ] }, { "page": "summarizeVariants-methods", "title": "Summarize variants by sample", "topics": [ "summarizeVariants", "summarizeVariants,GRangesList,VCF,function-method", "summarizeVariants,GRangesList,VCF,VariantType-method", "summarizeVariants,TxDb,VCF,CodingVariants-method", "summarizeVariants,TxDb,VCF,FiveUTRVariants-method", "summarizeVariants,TxDb,VCF,IntronVariants-method", "summarizeVariants,TxDb,VCF,PromoterVariants-method", "summarizeVariants,TxDb,VCF,SpliceSiteVariants-method", "summarizeVariants,TxDb,VCF,ThreeUTRVariants-method" ] }, { "page": "variant_body", "title": "helper function to construct inputs for VEP REST API", "topics": [ "variant_body" ] }, { "page": "defunct", "title": "Defunct Functions in Package 'VariantAnnotation'", "topics": [ "dbSNPFilter", "MatrixToSnpMatrix", "readVcfLongForm", "readVcfLongForm,character,character,missing-method", "readVcfLongForm,character,character,ScanVcfParam-method", "readVcfLongForm,character,missing,missing-method", "readVcfLongForm,TabixFile,character,GRanges-method", "readVcfLongForm,TabixFile,character,IntegerRangesList-method", "readVcfLongForm,TabixFile,character,missing-method", "readVcfLongForm,TabixFile,character,ScanVcfParam-method", "refLocsToLocalLocs", "refLocsToLocalLocs,GRanges,missing,GRangesList-method", "refLocsToLocalLocs,GRanges,TxDb,missing-method", "regionFilter", "restrictToSNV", "VariantAnnotation-defunct", "VRangesScanVcfParam" ] }, { "page": "VariantType-class", "title": "VariantType subclasses", "topics": [ "AllVariants", "AllVariants-class", "CodingVariants", "CodingVariants-class", "downstream", "downstream,AllVariants-method", "downstream,IntergenicVariants-method", "downstream,PromoterVariants-method", "downstream<-", "downstream<-,AllVariants-method", "downstream<-,IntergenicVariants-method", "downstream<-,PromoterVariants-method", "FiveUTRVariants", "FiveUTRVariants-class", "idType", "idType,IntergenicVariants-method", "idType<-", "idType<-,IntergenicVariants-method", "intergenic", "intergenic,AllVariants-method", "intergenic<-", "intergenic<-,AllVariants-method", "IntergenicVariants", "IntergenicVariants-class", "IntronVariants", "IntronVariants-class", "promoter", "promoter,AllVariants-method", "promoter<-", "promoter<-,AllVariants-method", "PromoterVariants", "PromoterVariants-class", "show,AllVariants-method", "show,PromoterVariants-method", "show,VariantType-method", "SpliceSiteVariants", "SpliceSiteVariants-class", "ThreeUTRVariants", "ThreeUTRVariants-class", "upstream", "upstream,AllVariants-method", "upstream,IntergenicVariants-method", "upstream,PromoterVariants-method", "upstream<-", "upstream<-,AllVariants-method", "upstream<-,IntergenicVariants-method", "upstream<-,PromoterVariants-method", "VariantType-class" ] }, { "page": "VCF-class", "title": "VCF class objects", "topics": [ "alt", "alt,VCF-method", "alt<-", "alt<-,CollapsedVCF,CharacterList-method", "alt<-,CollapsedVCF,DNAStringSetList-method", "alt<-,ExpandedVCF,character-method", "alt<-,ExpandedVCF,DNAStringSet-method", "cbind,VCF-method", "class:CollapsedVCF", "class:ExpandedVCF", "class:VCF", "CollapsedVCF", "CollapsedVCF-class", "dimnames<-,VCF,list-method", "expand,CollapsedVCF-method", "expand,ExpandedVCF-method", "ExpandedVCF", "ExpandedVCF-class", "filt", "filt,VCF-method", "filt<-", "filt<-,VCF,character-method", "fixed", "fixed,VCF-method", "fixed<-", "fixed<-,VCF,DataFrame-method", "geno", "geno,VCF,ANY-method", "geno,VCF,character-method", "geno,VCF,numeric-method", "geno,VCF-method", "geno,VCFHeader,ANY-method", "geno<-", "geno<-,VCF,character,matrix-method", "geno<-,VCF,missing,matrix-method", "geno<-,VCF,missing,SimpleList-method", "geno<-,VCF,numeric,matrix-method", "genome,VCF-method", "genotypeCodesToNucleotides", "header,VCF-method", "header<-", "header<-,VCF,VCFHeader-method", "info", "info,VCF-method", "info<-", "info<-,VCF,DataFrame-method", "mcols<-,VCF,ANY-method", "mcols<-,VCF-method", "qual", "qual,VCF-method", "qual<-", "qual<-,VCF,numeric-method", "rbind,VCF-method", "ref", "ref,VCF-method", "ref<-", "ref<-,VCF,DNAStringSet-method", "rowRanges,VCF-method", "rowRanges<-,VCF,GRanges-method", "seqlevels,VCF-method", "show,CollapsedVCF-method", "show,ExpandedVCF-method", "show,VCF-method", "SnpMatrixToVCF", "strand,VCF-method", "strand<-,VCF,ANY-method", "subset,VCF-method", "updateObject,VCF-method", "VCF", "VCF-class", "vcfFields,VCF-method", "[,VCF,ANY,ANY,ANY-method", "[,VCF,ANY,ANY-method", "[,VCF-method", "[<-,VCF,ANY,ANY,VCF-method" ] }, { "page": "VcfFile-class", "title": "Manipulate Variant Call Format (Vcf) files.", "topics": [ "vcfFields,character-method", "vcfFields,missing-method", "vcfFields,VcfFile-method", "vcfFields,VcfFileList-method", "VcfFile", "VcfFile-class", "VcfFileList", "VcfFileList-class" ] }, { "page": "VCFHeader-class", "title": "VCFHeader instances", "topics": [ "contig", "contig,VCFHeader-method", "fixed,VCFHeader-method", "fixed<-,VCFHeader,DataFrameList-method", "geno,VCFHeader-method", "geno<-,VCFHeader,missing,DataFrame-method", "header", "header,VCFHeader-method", "info,VCFHeader-method", "info<-,VCFHeader,DataFrame-method", "meta", "meta,VCFHeader-method", "meta<-", "meta<-,VCFHeader,DataFrame-method", "meta<-,VCFHeader,DataFrameList-method", "reference", "reference,VCFHeader-method", "samples", "samples,VCFHeader-method", "seqinfo,VCFHeader-method", "show,VCFHeader-method", "vcfFields", "vcfFields,VCFHeader-method", "VCFHeader", "VCFHeader-class" ] }, { "page": "vep_by_region", "title": "Use the VEP region API on variant information in a VCF object as defined in VariantAnnotation.", "topics": [ "vep_by_region" ] }, { "page": "VRanges-class", "title": "VRanges objects", "topics": [ "alt,VRanges-method", "alt<-,VRanges,ANY-method", "altDepth", "altDepth,VRanges-method", "altDepth<-", "altDepth<-,VRanges-method", "altFraction", "altFraction,VRanges-method", "asVCF", "asVCF,VRanges-method", "called", "called,VRanges-method", "characterOrRle-class", "characterRle-class", "class:VRanges", "coerce,GRanges,VRanges-method", "coerce,VCF,VRanges-method", "coerce,VRanges,VCF-method", "complexRle-class", "factorOrRle-class", "factorRle-class", "hardFilters", "hardFilters,VRanges-method", "hardFilters<-", "hardFilters<-,VRanges-method", "integerOrRle-class", "integerRle-class", "logicalRle-class", "makeVRangesFromGRanges", "match,VRanges,VRanges-method", "numericRle-class", "rawRle-class", "readVcfAsVRanges", "ref,VRanges-method", "ref<-,VRanges,ANY-method", "refDepth", "refDepth,VRanges-method", "refDepth<-", "refDepth<-,VRanges-method", "resetFilter", "sampleNames,VRanges-method", "sampleNames<-,VRanges,ANY-method", "softFilter", "softFilterMatrix", "softFilterMatrix,VRanges-method", "softFilterMatrix<-", "softFilterMatrix<-,VRanges-method", "tabulate", "tabulate,VRanges-method", "totalDepth", "totalDepth,VRanges-method", "totalDepth<-", "totalDepth<-,VRanges-method", "VRanges", "VRanges-class", "writeVcf,VRanges,ANY-method" ] }, { "page": "VRangesList-class", "title": "VRangesList objects", "topics": [ "alt,VRangesList-method", "class:CompressedVRangesList", "class:SimpleVRangesList", "class:VRangesList", "CompressedVRangesList-class", "ref,VRangesList-method", "SimpleVRangesList-class", "stackSamples", "stackSamples,VRangesList-method", "VRangesList", "VRangesList-class" ] }, { "page": "writeVcf-methods", "title": "Write VCF files", "topics": [ "writeVcf", "writeVcf,VCF,character-method", "writeVcf,VCF,connection-method" ] } ], "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "BSgenome", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "fastmap", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "glue", "httr", "IRanges", "jsonlite", "KEGGREST", "lambda.r", "lattice", "lifecycle", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pkgconfig", "png", "R6", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "SummarizedExperiment", "sys", "vctrs", "XML", "XVector", "yaml" ], "_sysdeps": [ { "shlib": "libcurl", "package": "libcurl4t64", "headers": "libcurl4-openssl-dev", "source": "curl", "version": "8.18.0-1ubuntu2.8", "name": "curl", "homepage": "https://curl.se/", "description": "easy-to-use client-side URL transfer library (OpenSSL flavour)" }, { "shlib": "libbz2", "package": "libbz2-1.0", "headers": "libbz2-dev", "source": "bzip2", "version": "1.0.8-6ubuntu0.1", "name": "bzip2", "homepage": "https://sourceware.org/bzip2/", "description": "high-quality block-sorting file compressor library - runtime" }, { "shlib": "liblzma", "package": "liblzma5", "headers": "liblzma-dev", "source": "xz-utils", "version": "5.8.3-1ubuntu0.1", "name": "xz-utils", "homepage": "https://tukaani.org/xz/", "description": "XZ-format compression library" }, { "shlib": "libz", "package": "zlib1g", "headers": "zlib1g-dev", "source": "zlib", "version": "1:1.3.dfsg+really1.3.1-1ubuntu3.2", "name": "zlib", "homepage": "http://zlib.net/", "description": "compression library - runtime" } ], "_score": 9.993934297924358, "_indexed": true, "_nocasepkg": "variantannotation", "_universes": [ "bioc", "bioconductor-bot" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.59.4", "date": "2026-11-07T12:35:14.000Z", "distro": "resolute", "arch": "aarch64", "commit": "6ab3a56c164777962b309123ef993ae6b45c405c", "fileid": "https://r2.ropensci.org/256c0bbb5e63cc896425946146d82fdd414bed6932870f5ceefb89627e805946", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42372061105" }, { "r": "4.7.0", "os": "linux", "version": "1.59.4", "date": "2026-11-07T12:37:29.000Z", "distro": "resolute", "arch": "x86_64", "commit": "6ab3a56c164777962b309123ef993ae6b45c405c", "fileid": "https://r2.ropensci.org/58632942e14cdc61f1d99ea2377d34607484b73c9b901dc4ec34885ba38aef08", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42372061105" }, { "r": "4.6.2", "os": "linux", "version": "1.59.4", "date": "2026-11-07T12:35:10.000Z", "distro": "resolute", "arch": "aarch64", "commit": "6ab3a56c164777962b309123ef993ae6b45c405c", "fileid": "https://r2.ropensci.org/4d9a4ceca8aa9c3f299f27b1e43a90a402765cae1c62610e8124b4c7357431fa", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42372061105" }, { "r": "4.6.2", "os": "linux", "version": "1.59.4", "date": "2026-11-07T12:37:16.000Z", "distro": "resolute", "arch": "x86_64", "commit": "6ab3a56c164777962b309123ef993ae6b45c405c", "fileid": "https://r2.ropensci.org/57391a45aebb44870a13f98d57b554bd041bd34d82a0a1cd2d8b3d2b9c6beea4", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42372061105" }, { "r": "4.5.3", "os": "mac", "version": "1.59.4", "date": "2026-11-07T12:37:46.000Z", "arch": "aarch64", "commit": "6ab3a56c164777962b309123ef993ae6b45c405c", "fileid": "https://r2.ropensci.org/ed458c6300dbb1f3321011818dd55d86a09fb98b27ef1176145a9ed5cccdd40a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42372061105" }, { "r": "4.5.3", "os": "mac", "version": "1.59.4", "date": "2026-11-07T12:41:51.000Z", "arch": "x86_64", "commit": "6ab3a56c164777962b309123ef993ae6b45c405c", "fileid": "https://r2.ropensci.org/bcaad772c3a75f8a28d7676f3fc4d8445ced437f37707d84b11492739c73bcac", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42372061105" }, { "r": "4.6.2", "os": "mac", "version": "1.59.4", "date": "2026-11-07T12:38:03.000Z", "arch": "aarch64", "commit": "6ab3a56c164777962b309123ef993ae6b45c405c", "fileid": "https://r2.ropensci.org/14a389815193b1fdfde5ee3f09fa83d0f549dd3b8654baae135967ee16ba4eab", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42372061105" }, { "r": "4.6.2", "os": "mac", "version": "1.59.4", "date": "2026-11-07T12:38:27.000Z", "arch": "x86_64", "commit": "6ab3a56c164777962b309123ef993ae6b45c405c", "fileid": "https://r2.ropensci.org/5101194e171580f60eb78ed05ab1373bc028a6bcc465853ec65ff28c654f141c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42372061105" }, { "r": "4.6.0", "os": "wasm", "version": "1.59.4", "date": "2026-11-07T12:34:34.000Z", "arch": "emscripten", "commit": "6ab3a56c164777962b309123ef993ae6b45c405c", "fileid": "https://r2.ropensci.org/f9b3cbd2ac92b552b045a561725cfb83e6493d6ede8e349633914d39a96a2e98", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42372061105" }, { "r": "4.7.0", "os": "win", "version": "1.59.4", "date": "2026-11-07T12:36:08.000Z", "arch": "aarch64", "commit": "6ab3a56c164777962b309123ef993ae6b45c405c", "fileid": "https://r2.ropensci.org/5af627556d022fcb68ccf61e4aebf2732aca5760aee8deff4f7418856130f9f9", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42372061105" }, { "r": "4.7.0", "os": "win", "version": "1.59.4", "date": "2026-11-07T12:34:49.000Z", "arch": "x86_64", "commit": "6ab3a56c164777962b309123ef993ae6b45c405c", "fileid": "https://r2.ropensci.org/09da9b6de4fc9f9fa12dd79180223c44a83008a66740c56b2ca16609d2fc026d", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42372061105" }, { "r": "4.5.3", "os": "win", "version": "1.59.4", "date": "2026-11-07T12:34:49.000Z", "arch": "x86_64", "commit": "6ab3a56c164777962b309123ef993ae6b45c405c", "fileid": "https://r2.ropensci.org/f7bcbc765a36f20a9194ed4d30f7454282a53f7423ba9fbd05ba6f661f0abf57", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42372061105" }, { "r": "4.6.2", "os": "win", "version": "1.59.4", "date": "2026-11-07T12:35:46.000Z", "arch": "aarch64", "commit": "6ab3a56c164777962b309123ef993ae6b45c405c", "fileid": "https://r2.ropensci.org/d9f73170248ff07b05d72de8234e63be937409c65bcc77822e3b2e82964fcff9", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42372061105" }, { "r": "4.6.2", "os": "win", "version": "1.59.4", "date": "2026-11-07T12:34:55.000Z", "arch": "x86_64", "commit": "6ab3a56c164777962b309123ef993ae6b45c405c", "fileid": "https://r2.ropensci.org/466d83e5b4dbd08fb05af229d3c1de0108fbe9fa4983d66a8042f39401296250", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42372061105" } ] }