{ "_id": "6a258757794753ddbc3de13c", "Package": "MultipleAlignment", "Title": "Representation of multiple sequence alignments in Bioconductor", "Description": "The package implements a set of S4 classes\n(DNAMultipleAlignment, RNAMultipleAlignment,\nAAMultipleAlignment) for representing Multiple Sequence\nAlignments (MSA). The classes allow users to represent groups\nof aligned DNA, RNA or amino acid sequences as a single object.\nThe package also provides functions to read/write such object\nfrom/to traditional MSA file formats including Stockholm and\nClustal.", "biocViews": "Alignment, MultipleSequenceAlignment, Genetics, DataImport,\nDataRepresentation, Infrastructure", "URL": "https://bioconductor.org/packages/MultipleAlignment", "BugReports": "https://github.com/Bioconductor/MultipleAlignment/issues", "Version": "0.99.4", "License": "Artistic-2.0", "Encoding": "UTF-8", "Authors@R": "c(\nperson(\"Marc\", \"Carlson\", role=\"aut\"),\nperson(\"Patrick\", \"Aboyoun\", role=\"aut\"),\nperson(\"Hervé\", \"Pagès\", role=\"cre\",\nemail=\"hpages.on.github@gmail.com\",\ncomment=c(ORCID=\"0009-0002-8272-4522\")),\nperson(\"Beryl\", \"Kanali\", role=\"ctb\",\ncomment=\"Converted 'MultipleAlignments' vignette from Sweave to RMarkdown\"),\nperson(\"Michael\", \"Lawrence\", role=\"ctb\"),\nperson(\"Martin\", \"Morgan\", role=\"ctb\"))", "VignetteBuilder": "knitr", "Collate": "MultipleAlignment-class.R MultipleAlignment-IO.R\nMultipleAlignment-utils.R", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-06-06 07:22:48 UTC", "RemoteUrl": "https://github.com/bioc/MultipleAlignment", "RemoteRef": "HEAD", "RemoteSha": "a3f8b65658f35937b23c0480d3fdd381376246f9", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-07 14:55:15 UTC", "User": "root" }, "Author": "Marc Carlson [aut],\nPatrick Aboyoun [aut],\nHervé Pagès [cre] (ORCID: ),\nBeryl Kanali [ctb] (Converted 'MultipleAlignments' vignette from Sweave\nto RMarkdown),\nMichael Lawrence [ctb],\nMartin Morgan [ctb]", "Maintainer": "Hervé Pagès ", "MD5sum": "039ce779fd1b1cd0b04e5713b4298aed", "_user": "bioc", "_type": "src", "_file": "MultipleAlignment_0.99.4.tar.gz", "_fileid": "51c3a276b14265fc0d18ae2724ecf5cee2368e9ebc0e03810f9ae33be680cf68", "_filesize": 192239, "_sha256": "51c3a276b14265fc0d18ae2724ecf5cee2368e9ebc0e03810f9ae33be680cf68", "_created": "2026-06-07T14:55:15.000Z", "_published": "2026-06-07T14:59:35.350Z", "_jobs": [ { "job": 79968116212, "time": 163, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7465242575" }, { "job": 79968116231, "time": 156, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7465241663" }, { "job": 79968116222, "time": 217, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7465249078" }, { "job": 79968116210, "time": 103, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7465235299" }, { "job": 79968116227, "time": 154, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7465241291" }, { "job": 79967919948, "time": 178, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7465221644" }, { "job": 79968116217, "time": 105, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7465235608" }, { "job": 79968116240, "time": 125, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7465237951" }, { "job": 79968116236, "time": 103, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7465235493" }, { "job": 79968116228, "time": 108, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7465235923" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 6 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/27095897388", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/MultipleAlignment", "_commit": { "id": "a3f8b65658f35937b23c0480d3fdd381376246f9", "author": "Hervé Pagès ", "committer": "Hervé Pagès ", "message": "define updateObject() methods for MultipleAlignment derivatives\n", "time": 1780730568 }, "_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": "BiocGenerics", "version": ">= 0.59.7", "role": "Depends" }, { "package": "S4Vectors", "role": "Depends" }, { "package": "IRanges", "role": "Depends" }, { "package": "Seqinfo", "role": "Depends" }, { "package": "Biostrings", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "pwalign", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2026-18", "n": 3 }, { "week": "2026-19", "n": 4 }, { "week": "2026-23", "n": 3 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "0.99.3", "bioc": "3.24" } ], "_topics": [ "alignment", "multiplesequencealignment", "genetics", "dataimport", "datarepresentation", "infrastructure", "bioconductor-package", "core-package" ], "_stars": 0, "_contributors": [ { "user": "hpages", "count": 10, "uuid": 8810451 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/bioconductor/multiplealignment", "_searchresults": 3, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MultipleAlignment.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/bioconductor/multiplealignment", "_realowner": "bioc", "_cranurl": false, "_exports": [ "AAMultipleAlignment", "alphabetFrequency", "as.matrix", "coerce", "colmask", "colmask<-", "consensusMatrix", "consensusString", "consensusViews", "detail", "DNAMultipleAlignment", "maskeddim", "maskedncol", "maskednrow", "maskedratio", "maskGaps", "maskMotif", "nchar", "ncol", "nrow", "readAAMultipleAlignment", "readDNAMultipleAlignment", "readRNAMultipleAlignment", "RNAMultipleAlignment", "rowmask", "rowmask<-", "rownames", "seqtype", "show", "unmasked", "updateObject", "write.phylip" ], "_help": [ { "page": "detail", "title": "Show (display) detailed object content", "topics": [ "detail" ] }, { "page": "MultipleAlignment-class", "title": "MultipleAlignment objects", "topics": [ "AAMultipleAlignment", "AAMultipleAlignment-class", "as.character,MultipleAlignment-method", "as.matrix,MultipleAlignment-method", "class:AAMultipleAlignment", "class:DNAMultipleAlignment", "class:MultipleAlignment", "class:RNAMultipleAlignment", "coerce,character,AAMultipleAlignment-method", "coerce,character,DNAMultipleAlignment-method", "coerce,character,RNAMultipleAlignment-method", "coerce,MultipleAlignment,AAStringSet-method", "coerce,MultipleAlignment,BStringSet-method", "coerce,MultipleAlignment,DNAStringSet-method", "coerce,MultipleAlignment,RNAStringSet-method", "colmask", "colmask,MultipleAlignment-method", "colmask<-", "colmask<-,MultipleAlignment,ANY-method", "colmask<-,MultipleAlignment,NULL-method", "detail,MultipleAlignment-method", "dim,MultipleAlignment-method", "DNAMultipleAlignment", "DNAMultipleAlignment-class", "maskeddim", "maskeddim,MultipleAlignment-method", "maskedncol", "maskedncol,MultipleAlignment-method", "maskednrow", "maskednrow,MultipleAlignment-method", "maskedratio,MultipleAlignment-method", "maskGaps", "maskGaps,MultipleAlignment-method", "maskMotif,MultipleAlignment,ANY-method", "MultipleAlignment", "MultipleAlignment-class", "nchar,MultipleAlignment-method", "ncol,MultipleAlignment-method", "nrow,MultipleAlignment-method", "RNAMultipleAlignment", "RNAMultipleAlignment-class", "rowmask", "rowmask,MultipleAlignment-method", "rowmask<-", "rowmask<-,MultipleAlignment,ANY-method", "rowmask<-,MultipleAlignment,NULL-method", "rownames,MultipleAlignment-method", "rownames<-,MultipleAlignment-method", "seqtype,MultipleAlignment-method", "show,MultipleAlignment-method", "unmasked,MultipleAlignment-method", "updateObject,AAMultipleAlignment-method", "updateObject,DNAMultipleAlignment-method", "updateObject,RNAMultipleAlignment-method" ] }, { "page": "MultipleAlignment-IO", "title": "Read/write MultipleAlignment objects", "topics": [ "MultipleAlignment-IO", "MultipleAlignment_IO", "readAAMultipleAlignment", "readDNAMultipleAlignment", "readRNAMultipleAlignment", "write.phylip" ] }, { "page": "MultipleAlignment-utils", "title": "MultipleAlignment utilities", "topics": [ "alphabetFrequency,MultipleAlignment-method", "consensusMatrix,MultipleAlignment-method", "consensusString,AAMultipleAlignment-method", "consensusString,DNAMultipleAlignment-method", "consensusString,MultipleAlignment-method", "consensusString,RNAMultipleAlignment-method", "consensusViews", "consensusViews,AAMultipleAlignment-method", "consensusViews,DNAMultipleAlignment-method", "consensusViews,MultipleAlignment-method", "consensusViews,RNAMultipleAlignment-method", "MultipleAlignment-utils", "MultipleAlignment_utils" ] } ], "_readme": "https://github.com/bioc/MultipleAlignment/raw/HEAD/README.md", "_rundeps": [ "BiocGenerics", "Biostrings", "crayon", "generics", "IRanges", "S4Vectors", "Seqinfo", "XVector" ], "_vignettes": [ { "source": "MultipleAlignments.Rmd", "filename": "MultipleAlignments.html", "title": "MultipleAlignment Objects", "author": "Marc Carlson, Beryl Kanali", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Creation and masking", "Analytic utilities", "Exporting to file", "Session Information" ], "created": "2026-04-30 00:33:16", "modified": "2026-04-30 00:33:16", "commits": 1 } ], "_score": 4.653212513775344, "_indexed": true, "_nocasepkg": "multiplealignment", "_universes": [ "bioc", "hpages", "bioconductor" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.4", "date": "2026-06-07T14:57:24.000Z", "distro": "noble", "commit": "a3f8b65658f35937b23c0480d3fdd381376246f9", "fileid": "c11f7a126746c01682a896eb575813d69df246644d005f566f2afb309615d5a8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27095897388" }, { "r": "4.6.0", "os": "linux", "version": "0.99.4", "date": "2026-06-07T14:58:12.000Z", "distro": "noble", "commit": "a3f8b65658f35937b23c0480d3fdd381376246f9", "fileid": "93f0189ffe2aa794bac564f6f14a27dc80f4768310ae757968b2bd6c0945a0cd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27095897388" }, { "r": "4.5.3", "os": "mac", "version": "0.99.4", "date": "2026-06-07T14:56:48.000Z", "commit": "a3f8b65658f35937b23c0480d3fdd381376246f9", "fileid": "99612f3ce224f7a1755caec5a30ed780426242129d3db493e19024dd2dda4359", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27095897388" }, { "r": "4.6.0", "os": "mac", "version": "0.99.4", "date": "2026-06-07T14:57:19.000Z", "commit": "a3f8b65658f35937b23c0480d3fdd381376246f9", "fileid": "b911917bc606674c95e809ab0b7b3029cddcb98649939257f64611e54a2477ad", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27095897388" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.4", "date": "2026-06-07T14:57:23.000Z", "commit": "a3f8b65658f35937b23c0480d3fdd381376246f9", "fileid": "7707c7d29a59f58984e3f5bdf01bf97c120e0d255fc13e1ba61f4f66607623df", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27095897388" }, { "r": "4.7.0", "os": "win", "version": "0.99.4", "date": "2026-06-07T14:56:40.000Z", "commit": "a3f8b65658f35937b23c0480d3fdd381376246f9", "fileid": "e92d02b40687cd3e1ef94fb59e72abb22c3c68cec131121ef68f58b7234a90fa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27095897388" }, { "r": "4.5.3", "os": "win", "version": "0.99.4", "date": "2026-06-07T14:56:43.000Z", "commit": "a3f8b65658f35937b23c0480d3fdd381376246f9", "fileid": "d1acd66f01c38ea0b33921ebe1b2c2e9495952d83ecde9081d46254f79cd3465", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27095897388" }, { "r": "4.6.0", "os": "win", "version": "0.99.4", "date": "2026-06-07T14:56:27.000Z", "commit": "a3f8b65658f35937b23c0480d3fdd381376246f9", "fileid": "650c9a3c07676c815a2df3253d134b9b76cd864203762a12782743538cd03ec1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27095897388" } ] }