{ "_id": "6a198326acfb0bcc41dfa3ca", "Package": "Seqinfo", "Title": "A simple S4 class for storing basic information about a\ncollection of genomic sequences", "Description": "The Seqinfo class stores the names, lengths, circularity\nflags, and genomes for a particular collection of sequences.\nThese sequences are typically the chromosomes and/or scaffolds\nof a specific genome assembly of a given organism. Seqinfo\nobjects are rarely used as standalone objects. Instead, they\nare used as part of higher-level objects to represent their\nseqinfo() component. Examples of such higher-level objects are\nGRanges, RangedSummarizedExperiment, VCF, GAlignments, etc...\ndefined in other Bioconductor infrastructure packages.", "biocViews": "Infrastructure, DataRepresentation, GenomeAssembly,\nAnnotation, GenomeAnnotation", "URL": "https://bioconductor.org/packages/Seqinfo", "BugReports": "https://github.com/Bioconductor/Seqinfo/issues", "Version": "1.3.0", "License": "Artistic-2.0", "Encoding": "UTF-8", "Authors@R": "person(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"),\nemail=\"hpages.on.github@gmail.com\",\ncomment=c(ORCID=\"0009-0002-8272-4522\"))", "VignetteBuilder": "knitr", "Collate": "utils.R rankSeqlevels.R seqinfo.R sortSeqlevels.R\nSeqinfo-class.R seqlevelsInUse.R GenomeDescription-class.R\nzzz.R", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:05:07 UTC", "RemoteUrl": "https://github.com/bioc/Seqinfo", "RemoteRef": "HEAD", "RemoteSha": "0dcd005b4ffe80c8864132d7db35451f67469d23", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 10:30:16 UTC", "User": "root" }, "Author": "Hervé Pagès [aut, cre] (ORCID: )", "Maintainer": "Hervé Pagès ", "MD5sum": "c96ba7eb158f2122a493016cb34e6104", "_user": "bioc", "_type": "src", "_file": "Seqinfo_1.3.0.tar.gz", "_fileid": "6278f50ce9cf88f7b0249aff47bf8a626a94c1de7571453875ddc0b9b11258a1", "_filesize": 192322, "_sha256": "6278f50ce9cf88f7b0249aff47bf8a626a94c1de7571453875ddc0b9b11258a1", "_created": "2026-05-29T10:30:16.000Z", "_published": "2026-05-29T12:14:30.029Z", "_jobs": [ { "job": 78483699839, "time": 240, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7288683541" }, { "job": 78483699817, "time": 350, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7288714239" }, { "job": 78483699850, "time": 340, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7288711539" }, { "job": 78483699807, "time": 232, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7290381779" }, { "job": 78483699833, "time": 201, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7290375302" }, { "job": 78482898179, "time": 335, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7288613977" }, { "job": 78483699809, "time": 268, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7288691238" }, { "job": 78483699834, "time": 214, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7288676560" }, { "job": 78483699849, "time": 216, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7288676777" }, { "job": 78483699843, "time": 220, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7288678306" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26631981920", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/Seqinfo", "_commit": { "id": "0dcd005b4ffe80c8864132d7db35451f67469d23", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381507 }, "_maintainer": { "name": "Hervé Pagès", "email": "hpages.on.github@gmail.com", "login": "hpages", "linkedin": "in/hervé-pagès-5038527", "description": "", "uuid": 8810451 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "methods", "role": "Depends" }, { "package": "BiocGenerics", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "S4Vectors", "version": ">= 0.47.6", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Suggests" }, { "package": "GenomicRanges", "role": "Suggests" }, { "package": "BSgenome", "role": "Suggests" }, { "package": "GenomicFeatures", "role": "Suggests" }, { "package": "TxDb.Hsapiens.UCSC.hg38.knownGene", "role": "Suggests" }, { "package": "TxDb.Dmelanogaster.UCSC.dm3.ensGene", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg38", "role": "Suggests" }, { "package": "BSgenome.Celegans.UCSC.ce2", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1789, "_updates": [ { "week": "2025-23", "n": 2 }, { "week": "2025-25", "n": 1 }, { "week": "2025-30", "n": 1 }, { "week": "2025-43", "n": 2 }, { "week": "2025-44", "n": 3 }, { "week": "2026-18", "n": 3 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.3.0", "bioc": "3.24" }, { "branch": "release", "version": "1.2.0", "bioc": "3.23" } ], "_topics": [ "infrastructure", "datarepresentation", "genomeassembly", "annotation", "genomeannotation", "bioconductor-package", "core-package" ], "_stars": 1, "_contributors": [ { "user": "hpages", "count": 12, "uuid": 8810451 }, { "user": "jwokaty", "count": 4, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 61323, "source": "https://www.bioconductor.org/packages/stats/bioc/Seqinfo" }, "_devurl": "https://github.com/bioconductor/seqinfo", "_searchresults": 26, "_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/readme.html", "extra/readme.md", "extra/Seqinfo.html", "manual.pdf" ], "_homeurl": "https://github.com/bioconductor/seqinfo", "_realowner": "bioc", "_cranurl": false, "_exports": [ "as.data.frame", "as.data.frame.Seqinfo", "bsgenomeName", "checkCompatibleSeqinfo", "commonName", "genome", "genome<-", "GenomeDescription", "intersect", "isCircular", "isCircular<-", "merge", "merge.Seqinfo", "orderSeqlevels", "organism", "provider", "providerVersion", "rankSeqlevels", "releaseDate", "restoreSeqlevels", "seqinfo", "Seqinfo", "seqinfo<-", "seqlengths", "seqlengths<-", "seqlevels", "seqlevels<-", "seqlevels0", "seqlevelsInUse", "seqnames", "seqnames<-", "show", "sortSeqlevels", "summary", "summary.Seqinfo", "update", "update.Seqinfo", "updateObject" ], "_help": [ { "page": "GenomeDescription-class", "title": "GenomeDescription objects", "topics": [ "bsgenomeName", "bsgenomeName,GenomeDescription-method", "class:GenomeDescription", "commonName", "commonName,GenomeDescription-method", "GenomeDescription", "GenomeDescription-class", "organism", "organism,GenomeDescription-method", "provider", "provider,GenomeDescription-method", "providerVersion", "providerVersion,GenomeDescription-method", "releaseDate", "releaseDate,GenomeDescription-method", "seqinfo,GenomeDescription-method", "seqnames,GenomeDescription-method", "show,GenomeDescription-method", "species", "species,GenomeDescription-method" ] }, { "page": "rankSeqlevels", "title": "Assign sequence IDs to sequence names", "topics": [ "orderSeqlevels", "rankSeqlevels" ] }, { "page": "seqinfo", "title": "Accessing/modifying sequence information", "topics": [ "genome", "genome,ANY-method", "genome<-", "genome<-,ANY-method", "isCircular", "isCircular,ANY-method", "isCircular<-", "isCircular<-,ANY-method", "restoreSeqlevels", "seqinfo", "seqinfo<-", "seqlengths", "seqlengths,ANY-method", "seqlengths<-", "seqlengths<-,ANY-method", "seqlevels", "seqlevels,ANY-method", "seqlevels0", "seqlevels<-", "seqlevels<-,ANY-method", "seqnames", "seqnames<-" ] }, { "page": "Seqinfo-class", "title": "Seqinfo objects", "topics": [ "as.data.frame,Seqinfo-method", "as.data.frame.Seqinfo", "checkCompatibleSeqinfo", "class:Seqinfo", "coerce,data.frame,Seqinfo-method", "coerce,DataFrame,Seqinfo-method", "genome,Seqinfo-method", "genome<-,Seqinfo-method", "intersect,Seqinfo,Seqinfo-method", "isCircular,Seqinfo-method", "isCircular<-,Seqinfo-method", "length,Seqinfo-method", "merge,missing,Seqinfo-method", "merge,NULL,Seqinfo-method", "merge,Seqinfo,missing-method", "merge,Seqinfo,NULL-method", "merge,Seqinfo,Seqinfo-method", "merge.Seqinfo", "names,Seqinfo-method", "names<-,Seqinfo-method", "Seqinfo", "Seqinfo-class", "seqlengths,Seqinfo-method", "seqlengths<-,Seqinfo-method", "seqlevels,Seqinfo-method", "seqlevels<-,Seqinfo-method", "seqnames,Seqinfo-method", "seqnames<-,Seqinfo-method", "show,Seqinfo-method", "summary,Seqinfo-method", "summary.Seqinfo", "update,Seqinfo-method", "update.Seqinfo", "updateObject,Seqinfo-method", "[,Seqinfo-method" ] }, { "page": "seqlevelsInUse", "title": "Get the sequence levels in use", "topics": [ "seqlevelsInUse", "seqlevelsInUse,CompressedList-method", "seqlevelsInUse,Vector-method" ] }, { "page": "sortSeqlevels", "title": "Sort the sequence levels of an object", "topics": [ "sortSeqlevels", "sortSeqlevels,ANY-method", "sortSeqlevels,character-method" ] } ], "_readme": "https://github.com/bioc/Seqinfo/raw/HEAD/README.md", "_rundeps": [ "BiocGenerics", "generics", "IRanges", "S4Vectors" ], "_vignettes": [ { "source": "Seqinfo.Rmd", "filename": "Seqinfo.html", "title": "The Seqinfo package", "author": "Hervé Pagès", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Install and load the package", "The Seqinfo constructor", "Seqinfo accessors", "Operations on Seqinfo objects", "Subset by seqnames", "Rename, drop, add and/or reorder the sequences", "Merge Seqinfo objects", "Seqinfo objects as parts of higher-level objects", "Session information" ], "created": "2025-04-29 01:41:53", "modified": "2025-06-03 16:08:56", "commits": 5 } ], "_score": 10.409449590923973, "_indexed": true, "_nocasepkg": "seqinfo", "_universes": [ "bioc", "hpages", "bioconductor" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.0", "date": "2026-05-29T10:35:44.000Z", "distro": "noble", "commit": "0dcd005b4ffe80c8864132d7db35451f67469d23", "fileid": "ae9a059ea69c817f05dad523994c9f6b07083d01bd27c61fcec32dfb135056a2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631981920" }, { "r": "4.6.0", "os": "linux", "version": "1.3.0", "date": "2026-05-29T10:35:39.000Z", "distro": "noble", "commit": "0dcd005b4ffe80c8864132d7db35451f67469d23", "fileid": "f9a3b4c20279e60c44ee71d26afdd7a67ce017a42e767837dfe6e37985eb1189", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631981920" }, { "r": "4.5.3", "os": "mac", "version": "1.3.0", "date": "2026-05-29T12:13:42.000Z", "commit": "0dcd005b4ffe80c8864132d7db35451f67469d23", "fileid": "04f6bf1c932de604205b2db8bbb2d1547e3a9fd07119e0d4eeca8c7cb38a8a58", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631981920" }, { "r": "4.6.0", "os": "mac", "version": "1.3.0", "date": "2026-05-29T12:13:11.000Z", "commit": "0dcd005b4ffe80c8864132d7db35451f67469d23", "fileid": "38bda8af1ad5122564ff2684417d374d0961c3dc16920aaec98c2a0a86066823", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631981920" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.0", "date": "2026-05-29T10:35:09.000Z", "commit": "0dcd005b4ffe80c8864132d7db35451f67469d23", "fileid": "311270abe0a8a22c4916ab99a551238a6df96e85e092e6eef3a0ccf79ffbaad7", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631981920" }, { "r": "4.7.0", "os": "win", "version": "1.3.0", "date": "2026-05-29T10:33:13.000Z", "commit": "0dcd005b4ffe80c8864132d7db35451f67469d23", "fileid": "7cd1e5ba41b6102ebb23fde3a76113430277ccf4051213712307a93f161c9540", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631981920" }, { "r": "4.5.3", "os": "win", "version": "1.3.0", "date": "2026-05-29T10:33:26.000Z", "commit": "0dcd005b4ffe80c8864132d7db35451f67469d23", "fileid": "54c6fd79f3042b09e848166bc63b7d2c8f10e9e78eba25500b4cbea7f8fe12bd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631981920" }, { "r": "4.6.0", "os": "win", "version": "1.3.0", "date": "2026-05-29T10:33:30.000Z", "commit": "0dcd005b4ffe80c8864132d7db35451f67469d23", "fileid": "92cefbedef102b8e162690c08150903b1ab966f29c813d61a9cb11f38aa231f3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631981920" } ] }