{ "_id": "6a49434818cdde069385eab7", "Package": "odseq", "Type": "Package", "Title": "Outlier detection in multiple sequence alignments", "Version": "1.41.0", "Date": "2015-12-20", "Author": "José Jiménez", "Maintainer": "José Jiménez ", "Description": "Performs outlier detection of sequences in a multiple\nsequence alignment using bootstrap of predefined distance\nmetrics. Outlier sequences can make downstream analyses\nunreliable or make the alignments less accurate while they are\nbeing constructed. This package implements the OD-seq algorithm\nproposed by Jehl et al (doi 10.1186/s12859-015-0702-1) for\naligned sequences and a variant using string kernels for\nunaligned sequences.", "License": "MIT + file LICENSE", "LazyData": "True", "Encoding": "UTF-8", "biocViews": "Alignment, MultipleSequenceAlignment", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:43:15 UTC", "RemoteUrl": "https://github.com/bioc/odseq", "RemoteRef": "HEAD", "RemoteSha": "383178a721609e8091ea5e5d0ce4f94d3672dd8c", "Packaged": { "Date": "2026-07-04 12:14:36 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "odseq_1.41.0.tar.gz", "_fileid": "https://r2.ropensci.org/7e5d7ed8ee3344732479d3224b367e4ca1bb03cace462c5c27a21f7bb5f51bde", "_filesize": 141595, "_sha256": "7e5d7ed8ee3344732479d3224b367e4ca1bb03cace462c5c27a21f7bb5f51bde", "_expires": "2026-10-12T17:30:46.000Z", "_created": "2026-07-04T12:14:36.000Z", "_published": "2026-07-04T17:30:48.082Z", "_bioccheck": { "error": 2, "warning": 1, "note": 12 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28705799471", "_status": "success", "_upstream": "https://github.com/bioc/odseq", "_commit": { "id": "383178a721609e8091ea5e5d0ce4f94d3672dd8c", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380195 }, "_maintainer": { "name": "José Jiménez", "email": "jose@jimenezluna.com", "login": "josejimenezluna", "bluesky": "@jjimenezluna.bsky.social", "description": "Driving drug discovery one gradient update at a time.", "uuid": 6875576 }, "_distro": "resolute", "_jobs": [ { "job": 85152393487, "time": 174, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8081600907" }, { "job": 85152393449, "time": 236, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8081607324" }, { "job": 85152393567, "time": 302, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8081614543" }, { "job": 85152393334, "time": 142, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8081597677" }, { "job": 85152393655, "time": 145, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8081597924" }, { "job": 85152393219, "time": 192, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8081582458" }, { "job": 85152393541, "time": 134, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8081596936" }, { "job": 85152393290, "time": 144, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8081597839" }, { "job": 85152393577, "time": 157, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8081599244" }, { "job": 85152393406, "time": 151, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8081598812" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.2.3", "role": "Depends" }, { "package": "msa", "version": ">= 1.2.1", "role": "Imports" }, { "package": "kebabs", "version": ">= 1.4.1", "role": "Imports" }, { "package": "mclust", "version": ">= 5.1", "role": "Imports" }, { "package": "knitr", "version": ">= 1.11", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.41.0", "bioc": "3.24" }, { "branch": "release", "version": "1.40.0", "bioc": "3.23" } ], "_topics": [ "alignment", "multiplesequencealignment" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_searchresults": 29, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/odseq.html", "LICENSE", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "odmix", "odseq", "odseq_unaligned" ], "_datasets": [ { "name": "seqs", "title": "PFAM plus random data.", "object": "seqs", "class": [ "AAStringSet" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "odseq-package", "title": "Outlier detection in multiple sequence alignments", "topics": [ "odseq-package" ] }, { "page": "odmix", "title": "Gaussian mixture modelling of distances in a multiple sequence alignment.", "topics": [ "odmix" ] }, { "page": "odseq", "title": "Outlier detection in a multiple sequence alignment", "topics": [ "odseq" ] }, { "page": "odseq_unaligned", "title": "Outlier detection provided a distance/similarity matrix of sequences.", "topics": [ "odseq_unaligned" ] }, { "page": "seqs", "title": "PFAM plus random data.", "topics": [ "seqs" ] } ], "_rundeps": [ "apcluster", "BiocGenerics", "Biostrings", "class", "crayon", "e1071", "generics", "IRanges", "kebabs", "kernlab", "lattice", "LiblineaR", "MASS", "Matrix", "mclust", "msa", "MultipleAlignment", "proxy", "Rcpp", "S4Vectors", "Seqinfo", "XVector" ], "_vignettes": [ { "source": "vignette.Rmd", "filename": "vignette.html", "title": "odseq package vignette", "author": "Mantainer: jose@jimenezluna.com", "engine": "knitr::rmarkdown", "headings": [ "Aligned sequences", "Unaligned sequences" ], "created": "2016-03-31 20:34:14", "modified": "2016-03-31 20:34:14", "commits": 1 } ], "_score": 4.2405492482825995, "_indexed": true, "_nocasepkg": "odseq", "_universes": [ "bioc", "josejimenezluna" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.41.0", "date": "2026-07-04T12:17:19.000Z", "distro": "resolute", "commit": "383178a721609e8091ea5e5d0ce4f94d3672dd8c", "fileid": "https://r2.ropensci.org/311f67d8e48bc33feed3deb6967ce70dc2b83f353562d97c96ac832a7dfa7252", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28705799471" }, { "r": "4.6.1", "os": "linux", "version": "1.41.0", "date": "2026-07-04T12:18:22.000Z", "distro": "resolute", "commit": "383178a721609e8091ea5e5d0ce4f94d3672dd8c", "fileid": "https://r2.ropensci.org/c15dc4982c0fee7fdf23b67615b152e241b3ac0bdc6d3ac16b4a5fdf92ed2dcf", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28705799471" }, { "r": "4.5.3", "os": "mac", "version": "1.41.0", "date": "2026-07-04T12:16:19.000Z", "commit": "383178a721609e8091ea5e5d0ce4f94d3672dd8c", "fileid": "https://r2.ropensci.org/9fe75aa25c9c63a5a66dc1b14e40a048f3ba82d6ba605c88b129483ff46525ba", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28705799471" }, { "r": "4.6.1", "os": "mac", "version": "1.41.0", "date": "2026-07-04T12:16:13.000Z", "commit": "383178a721609e8091ea5e5d0ce4f94d3672dd8c", "fileid": "https://r2.ropensci.org/892038c425cb8f98eccb4ed3e35e6fb1e281b95ef9667263274fb9fdf9045ee7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28705799471" }, { "r": "4.6.0", "os": "wasm", "version": "1.41.0", "date": "2026-07-04T12:17:11.000Z", "commit": "383178a721609e8091ea5e5d0ce4f94d3672dd8c", "fileid": "https://r2.ropensci.org/46dab620c25422bcb788ebcae5deb382d70777b379965531c7f7ff2670707a36", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28705799471" }, { "r": "4.7.0", "os": "win", "version": "1.41.0", "date": "2026-07-04T12:15:48.000Z", "commit": "383178a721609e8091ea5e5d0ce4f94d3672dd8c", "fileid": "https://r2.ropensci.org/e38035e3480604d62c741ffd8ca99b740ef4163fa69890e39a3e79b4cbfb3069", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28705799471" }, { "r": "4.5.3", "os": "win", "version": "1.41.0", "date": "2026-07-04T12:15:53.000Z", "commit": "383178a721609e8091ea5e5d0ce4f94d3672dd8c", "fileid": "https://r2.ropensci.org/47fc060f3e96825ff7088517ad35441e00fe62622c0ed66703132591dbb631bd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28705799471" }, { "r": "4.6.1", "os": "win", "version": "1.41.0", "date": "2026-07-04T12:15:51.000Z", "commit": "383178a721609e8091ea5e5d0ce4f94d3672dd8c", "fileid": "https://r2.ropensci.org/34f42d9f6a6887f1f460dccf519bb40eca1d64dfc908c2faa189db2e1edbb11c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28705799471" } ] }