{ "_id": "6a1ad4801d7bb097a09e425f", "Package": "doubletrouble", "Title": "Identification and classification of duplicated genes", "Version": "1.13.0", "Date": "2024-03-19", "Authors@R": "c(\nperson(given = \"Fabrício\",\nfamily = \"Almeida-Silva\",\nrole = c(\"aut\", \"cre\"),\nemail = \"fabricio_almeidasilva@hotmail.com\",\ncomment = c(ORCID = \"0000-0002-5314-2964\")),\nperson(given = \"Yves\",\nfamily = \"Van de Peer\",\nrole = \"aut\",\nemail = \"yves.vandepeer@psb.vib-ugent.be\",\ncomment = c(ORCID = \"0000-0003-4327-3730\"))\n)", "Description": "doubletrouble aims to identify duplicated genes from\nwhole-genome protein sequences and classify them based on their\nmodes of duplication. The duplication modes are i. segmental\nduplication (SD); ii. tandem duplication (TD); iii. proximal\nduplication (PD); iv. transposed duplication (TRD) and; v.\ndispersed duplication (DD). Transposon-derived duplicates (TRD)\ncan be further subdivided into rTRD (retrotransposon-derived\nduplication) and dTRD (DNA transposon-derived duplication). If\nusers want a simpler classification scheme, duplicates can also\nbe classified into SD- and SSD-derived (small-scale\nduplication) gene pairs. Besides classifying gene pairs, users\ncan also classify genes, so that each gene is assigned a unique\nmode of duplication. Users can also calculate substitution\nrates per substitution site (i.e., Ka and Ks) from duplicate\npairs, find peaks in Ks distributions with Gaussian Mixture\nModels (GMMs), and classify gene pairs into age groups based on\nKs peaks.", "License": "GPL-3", "URL": "https://github.com/almeidasilvaf/doubletrouble", "BugReports": "https://support.bioconductor.org/t/doubletrouble", "biocViews": "Software, WholeGenome, ComparativeGenomics,\nFunctionalGenomics, Phylogenetics, Network, Classification", "Encoding": "UTF-8", "LazyData": "false", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libglpk-dev make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:59:27 UTC", "RemoteUrl": "https://github.com/bioc/doubletrouble", "RemoteRef": "HEAD", "RemoteSha": "4f93b41cf40a5ce957ea9bbc376510103e5193cf", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:40:13 UTC", "User": "root" }, "Author": "Fabrício Almeida-Silva [aut, cre] (ORCID:\n),\nYves Van de Peer [aut] (ORCID: )", "Maintainer": "Fabrício Almeida-Silva ", "MD5sum": "bc79288a8dbb5ecd550ca3b6550a807e", "_user": "bioc", "_type": "src", "_file": "doubletrouble_1.13.0.tar.gz", "_fileid": "1cabf7135a1a4015cff7989a1f49dbba42a99a0e15ae13380f9ea29f9e7c07e9", "_filesize": 5118405, "_sha256": "1cabf7135a1a4015cff7989a1f49dbba42a99a0e15ae13380f9ea29f9e7c07e9", "_created": "2026-05-30T08:40:13.000Z", "_published": "2026-05-30T12:13:52.167Z", "_jobs": [ { "job": 78637204655, "time": 217, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7306921374" }, { "job": 78637204682, "time": 474, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7306945695" }, { "job": 78637204665, "time": 444, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7306943007" }, { "job": 78637204673, "time": 253, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7308081602" }, { "job": 78637204705, "time": 287, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7308084560" }, { "job": 78636918177, "time": 359, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306899855" }, { "job": 78637204660, "time": 208, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306920375" }, { "job": 78637204698, "time": 519, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7306952862" }, { "job": 78637204687, "time": 333, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7306932412" }, { "job": 78637204672, "time": 329, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7306931946" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679365366", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/doubletrouble", "_commit": { "id": "4f93b41cf40a5ce957ea9bbc376510103e5193cf", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381167 }, "_maintainer": { "name": "Fabrício Almeida-Silva", "email": "fabricio_almeidasilva@hotmail.com", "login": "almeidasilvaf", "bluesky": "@almeidasilvaf.bsky.social", "description": "Bioinformatics. Network biology. 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"title": "Duplicate pairs and Ks values for Glycine max", "object": "gmax_ks", "file": "gmax_ks.rda", "class": [ "data.frame" ], "fields": [ "dup1", "dup2", "Ks", "type" ], "rows": 68463, "table": true, "tojson": true }, { "name": "yeast_annot", "title": "Genome annotation of the yeast species S. cerevisiae and C. glabrata", "object": "yeast_annot", "file": "yeast_annot.rda", "class": [ "CompressedGRangesList" ], "fields": [], "table": false, "tojson": false }, { "name": "yeast_seq", "title": "Protein sequences of the yeast species S. cerevisiae and C. glabrata", "object": "yeast_seq", "file": "yeast_seq.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "cds_scerevisiae", "title": "Coding sequences (CDS) of S. cerevisiae", "topics": [ "cds_scerevisiae" ] }, { "page": "classify_gene_pairs", "title": "Classify duplicate gene pairs based on their modes of duplication", "topics": [ "classify_gene_pairs" ] }, { "page": "classify_genes", 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