{ "_id": "6a193534acfb0bcc41dd225d", "Package": "VariantAnnotation", "Type": "Package", "Title": "Annotation of Genetic Variants", "Description": "Annotate variants, compute amino acid coding changes,\npredict coding outcomes.", "Version": "1.59.0", "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": "2026-04-28 12:35:39 UTC", "RemoteUrl": "https://github.com/bioc/VariantAnnotation", "RemoteRef": "HEAD", "RemoteSha": "708bb312c3867eafc39bdbf68dce74cc90df8304", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-29 06:10:31 UTC", "User": "root" }, "Author": "Valerie Oberchain [aut],\nMartin Morgan [aut],\nMichael Lawrence [aut],\nStephanie Gogarten [ctb],\nBioconductor Package Maintainer [cre]", "Maintainer": "Bioconductor Package Maintainer ", "MD5sum": "f7bac92aa7b9031b601b9923279d8b54", "_user": "bioc", "_type": "src", "_file": "VariantAnnotation_1.59.0.tar.gz", "_fileid": "fd54805e256173f88e35fe8e3b8a2dc8c69156b874a08264e8bbe80c1d321595", "_filesize": 1818736, "_sha256": "fd54805e256173f88e35fe8e3b8a2dc8c69156b874a08264e8bbe80c1d321595", "_created": "2026-05-29T06:10:31.000Z", "_published": "2026-05-29T06:41:56.134Z", "_jobs": [ { "job": 78447835418, "time": 464, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7284380523" }, { "job": 78447835541, "time": 738, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "7284443153" }, { "job": 78447835494, "time": 864, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7284472524" }, { "job": 78447835560, "time": 726, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7284440741" }, { "job": 78447835539, "time": 823, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7284462728" }, { "job": 78447835496, "time": 450, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7284537911" }, { "job": 78447835497, "time": 877, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7284644214" }, { "job": 78447835490, "time": 520, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7284541734" }, { "job": 78447835511, "time": 1048, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7284686525" }, { "job": 78446503760, "time": 720, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7284274009" }, { "job": 78447835419, "time": 377, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 78447835528, "time": 819, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7284462163" }, { "job": 78447835562, "time": 866, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7284473728" }, { "job": 78447835573, "time": 793, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7284456040" } ], "_bioccheck": { "error": 0, "warning": 3, "note": 20 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26620945575", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/VariantAnnotation", "_commit": { "id": "708bb312c3867eafc39bdbf68dce74cc90df8304", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379739 }, "_maintainer": { "name": "Bioconductor Package Maintainer", "email": "maintainer@bioconductor.org", "login": "bioconductor-bot", "description": "", "uuid": 11681645 }, "_distro": "noble", "_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": 156, "_updates": [ { "week": "2025-25", "n": 1 }, { "week": "2025-42", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2025-51", "n": 3 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.59.0", "bioc": "3.24" }, { "branch": "release", "version": "1.58.0", "bioc": "3.23" } ], "_topics": [ "dataimport", "sequencing", "snp", "annotation", "genetics", "variantannotation", "curl", "bzip2", "xz-utils", "zlib" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 15286, "source": "https://www.bioconductor.org/packages/stats/bioc/VariantAnnotation" }, "_mentions": 47, "_searchresults": 2184, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/VariantAnnotation.html", "manual.pdf" ], "_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": "8.5.0-2ubuntu10.9", "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": "1.0.8-5.1build0.1", "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": "5.6.1+really5.4.5-1ubuntu0.2", "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-3.1ubuntu2.1", "name": "zlib", "homepage": "http://zlib.net/", "description": "compression library - runtime" } ], "_vignettes": [ { "source": "VariantAnnotation.Rmd", "filename": "VariantAnnotation.html", "title": "Introduction to VariantAnnotation ", "author": "Valerie Obenchain", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Variant Call Format (VCF) files", "Data import and exploration", "Header information", "Genomic positions", "Genotype data", "Info data", "Import data subsets", "Select genomic coordinates", "Select VCF fields", "Locating variants in and around genes", "Amino acid coding changes", "SIFT and PolyPhen Databases", "Other operations", "Create a SnpMatrix", "Write out VCF files", "Performance", "References", "Session Information" ], "created": "2023-06-02 16:05:20", "modified": "2023-06-02 16:05:20", "commits": 1 }, { "source": "filterVcf.Rmd", "filename": "filterVcf.html", "title": "Using filterVcf() to Select Variants from VCF Files ", "author": "Paul Shannon", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "The Data: Paired Tumor/Normal Breast Cancer Variants", "Filter by Genomic Region", "Introducing the filterVcf Method", "Prefilters", "Filters", "FilterRules", "Create the Filtered file", "Look for SNPs in Regulatory Regions", "Load CTCF Transcription Factor Binding Regions Identified in MCF-7 Breast Cancer Cell Line", "Find SNPs in CTCF Binding Regions", "Conclusion", "Appendix: Filter by Genomic Region", "Bibliography" ], "created": "2023-06-02 16:05:20", "modified": "2023-06-02 16:05:20", "commits": 1 }, { "source": "ensemblVEP.Rmd", "filename": "ensemblVEP.html", "title": "ensemblVEP: using the REST API with Bioconductor", "author": "Vincent J. Carey, stvjc at channing.harvard.edu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Acquire annotation on variants from a VCF file", "Transforming the API response to GRanges", "Further work", "References" ], "created": "2024-01-26 10:38:58", "modified": "2024-01-26 10:38:58", "commits": 1 } ], "_score": 11.36988360141146, "_indexed": true, "_nocasepkg": "variantannotation", "_universes": [ "bioc", "bioconductor-bot" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.59.0", "date": "2026-05-29T06:18:32.000Z", "distro": "noble", "arch": "aarch64", "commit": "708bb312c3867eafc39bdbf68dce74cc90df8304", "fileid": "14f1e76e7c70dd2c957d72358a2ddced8c50b16497702591d7a1a018fb761f34", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26620945575" }, { "r": "4.7.0", "os": "linux", "version": "1.59.0", "date": "2026-05-29T06:19:42.000Z", "distro": "noble", "arch": "x86_64", "commit": "708bb312c3867eafc39bdbf68dce74cc90df8304", "fileid": "1f49a15555407ad63bbcb7f798f475a1673231cac2aedec0eddeff3d9fd1a1ff", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26620945575" }, { "r": "4.6.0", "os": "linux", "version": "1.59.0", "date": "2026-05-29T06:18:30.000Z", "distro": "noble", "arch": "aarch64", "commit": "708bb312c3867eafc39bdbf68dce74cc90df8304", "fileid": "183a9fca20c19e6f20cdd4199bc2bc20cacb9fde27c647559b9ae02bd93a7387", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26620945575" }, { "r": "4.6.0", "os": "linux", "version": "1.59.0", "date": "2026-05-29T06:19:19.000Z", "distro": "noble", "arch": "x86_64", "commit": "708bb312c3867eafc39bdbf68dce74cc90df8304", "fileid": "2543a393a9b5028276ddeabd45b8df26864eb96d4db74bc5cf014f39052a272f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26620945575" }, { "r": "4.5.3", "os": "mac", "version": "1.59.0", "date": "2026-05-29T06:26:46.000Z", "arch": "aarch64", "commit": "708bb312c3867eafc39bdbf68dce74cc90df8304", "fileid": "8f29958f44b821bd19de832a8e5d8245e4aad35d5562aea66c8fb13376e948ce", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26620945575" }, { "r": "4.5.3", "os": "mac", "version": "1.59.0", "date": "2026-05-29T06:30:07.000Z", "arch": "x86_64", "commit": "708bb312c3867eafc39bdbf68dce74cc90df8304", "fileid": "c98c7f50568a4f28531ed4ccfd25f0481cc2c8e468cfe80241c7c534ca4c7055", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26620945575" }, { "r": "4.6.0", "os": "mac", "version": "1.59.0", "date": "2026-05-29T06:26:24.000Z", "arch": "aarch64", "commit": "708bb312c3867eafc39bdbf68dce74cc90df8304", "fileid": "b62d72616231f8b61e0891eebda5b827353d6ed6464642432d8d6cbe8e2a4b4d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26620945575" }, { "r": "4.6.0", "os": "mac", "version": "1.59.0", "date": "2026-05-29T06:31:01.000Z", "arch": "x86_64", "commit": "708bb312c3867eafc39bdbf68dce74cc90df8304", "fileid": "0a34f04f60deb15b3919b77f981e62e22fdc9aac96b2e4f38e3cd6eb2a0bbb44", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26620945575" }, { "r": "4.7.0", "os": "win", "version": "1.59.0", "date": "2026-05-29T06:18:04.000Z", "arch": "x86_64", "commit": "708bb312c3867eafc39bdbf68dce74cc90df8304", "fileid": "9b7d20bc6f3b2a16c6db42b95eec3793412180218ab910b25bc93500e6755beb", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26620945575" }, { "r": "4.5.3", "os": "win", "version": "1.59.0", "date": "2026-05-29T06:18:00.000Z", "arch": "x86_64", "commit": "708bb312c3867eafc39bdbf68dce74cc90df8304", "fileid": "921de3eeff6456c6934b899278be436a9b8bf547389268cf6bccb3212189bb9f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26620945575" }, { "r": "4.6.0", "os": "win", "version": "1.59.0", "date": "2026-05-29T06:17:39.000Z", "arch": "x86_64", "commit": "708bb312c3867eafc39bdbf68dce74cc90df8304", "fileid": "383e549ca3c7460381da654fa79ad223bd73eb4234f59b8b564331cc89271edf", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26620945575" } ] }