{ "_id": "6a4f718021b18e1548501ea0", "Package": "SynMut", "Type": "Package", "Title": "SynMut: Designing Synonymously Mutated Sequences with Different\nGenomic Signatures", "Version": "1.29.0", "Authors@R": "c(person(\"Haogao\", \"Gu\", email = \"hggu@connect.hku.hk\", role = c(\"aut\", \"cre\")),\nperson(\"Leo L.M.\", \"Poon\", email = \"llmpoon@hku.hk\", role = \"led\"))", "Description": "There are increasing demands on designing virus mutants\nwith specific dinucleotide or codon composition. This tool can\ntake both dinucleotide preference and/or codon usage bias into\naccount while designing mutants. It is a powerful tool for in\nsilico designs of DNA sequence mutants.", "License": "GPL-2", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "7.1.0", "Collate": "'regioned_dna_Class.R' 'codon_mimic.R' 'input_seq.R'\n'codon_random.R' 'codon_to.R' 'dinu_to.R' 'distance_analysis.R'\n'region_related.R' 'seq_random.R' 'zzz.R'", "biocViews": "SequenceMatching, ExperimentalDesign, Preprocessing", "BugReports": "https://github.com/Koohoko/SynMut/issues", "URL": "https://github.com/Koohoko/SynMut", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:50:09 UTC", "RemoteUrl": "https://github.com/bioc/SynMut", "RemoteRef": "HEAD", "RemoteSha": "b50cc017ecd70430ec65a7ba695a5aeecfe5419b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-09 09:55:40 UTC", "User": "root" }, "Author": "Haogao Gu [aut, cre],\nLeo L.M. Poon [led]", "Maintainer": "Haogao Gu ", "_user": "bioc", "_type": "src", "_file": "SynMut_1.29.0.tar.gz", "_fileid": "https://r2.ropensci.org/8871c65e5700e425aa07c02197f01cd4b88ee14205a1263fc8d8938a94c6ec47", "_filesize": 152546, "_sha256": "8871c65e5700e425aa07c02197f01cd4b88ee14205a1263fc8d8938a94c6ec47", "_expires": "2026-10-17T10:01:34.000Z", "_created": "2026-07-09T09:55:40.000Z", "_published": "2026-07-09T10:01:36.584Z", "_bioccheck": { "error": 0, "warning": 1, "note": 8 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29009679252", "_status": "success", "_upstream": "https://github.com/bioc/SynMut", "_commit": { "id": "b50cc017ecd70430ec65a7ba695a5aeecfe5419b", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380609 }, "_maintainer": { "name": "Haogao Gu", "email": "hggu@connect.hku.hk", "login": "koohoko", "twitter": "@GuHaogao", "description": "Studying virus evolution and transmission.", "uuid": 11829095 }, "_distro": "resolute", "_jobs": [ { "job": 86090595695, "time": 190, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8195173062" }, { "job": 86090595712, "time": 278, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8195207503" }, { "job": 86090595687, "time": 269, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8195204545" }, { "job": 86090595674, "time": 125, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8195147253" }, { "job": 86090595680, "time": 142, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8195154009" }, { "job": 86089952980, "time": 204, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8195095669" }, { "job": 86090595650, "time": 148, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8195156447" }, { "job": 86090595744, "time": 146, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8195155939" }, { "job": 86090595727, "time": 181, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8195169613" }, { "job": 86090595752, "time": 167, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8195164520" } ], "_registered": true, "_dependencies": [ { "package": "seqinr", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "BiocManager", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" }, { "package": "prettydoc", "role": "Suggests" }, { "package": "glue", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.29.0", "bioc": "3.24" }, { "branch": "release", "version": "1.28.0", "bioc": "3.23" } ], "_topics": [ "sequencematching", "experimentaldesign", "preprocessing" ], "_stars": 2, "_contributors": [ { "user": "koohoko", "count": 75, "uuid": 11829095 }, { "user": "nturaga", "count": 14, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 364, "source": "https://www.bioconductor.org/packages/stats/bioc/SynMut" }, "_devurl": "https://github.com/koohoko/synmut", "_searchresults": 10, "_rbuild": "4.6.1", "_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/SynMut.html", "manual.pdf" ], "_homeurl": "https://github.com/koohoko/synmut", "_realowner": "bioc", "_cranurl": false, "_exports": [ "codon_dist", "codon_mimic", "codon_random", "codon_to", "dinu_dist", "dinu_to", "get_cu", "get_dna", "get_du", "get_freq", "get_nu", "get_region", "get_rscu", "input_seq", "seq_random" ], "_help": [ { "page": "codon_dist-methods", "title": "Calculating the codon usage difference between sequences", "topics": [ "codon_dist", "codon_dist,ANY-method" ] }, { "page": "codon_mimic-methods", "title": "Mimic a target codon usage bias", "topics": [ "codon_mimic", "codon_mimic,DNAStringSet,DNAStringSet-method", "codon_mimic,regioned_dna,DNAStringSet-method", "codon_mimic,regioned_dna,vector-method" ] }, { "page": "codon_random-methods", "title": "Generate random synonymous mutations", "topics": [ "codon_random", "codon_random,DNAStringSet-method", "codon_random,regioned_dna-method" ] }, { "page": "codon_to-methods", "title": "Maximize or minimize the usage of certain codon.", "topics": [ "codon_to", "codon_to,regioned_dna-method" ] }, { "page": "dinu_dist-methods", "title": "Calculating the dinucleotide usage difference between sequences", "topics": [ "dinu_dist", "dinu_dist,ANY-method" ] }, { "page": "dinu_to-methods", "title": "Maximize or minimize the usage of certain dinucleotide.", "topics": [ "dinu_to", "dinu_to,regioned_dna-method" ] }, { "page": "get_cu-methods", "title": "Get codon usage matrix", "topics": [ "get_cu", "get_cu,DNAStringSet-method", "get_cu,regioned_dna-method" ] }, { "page": "get_dna-methods", "title": "Get the DNAStringSet data", "topics": [ "get_dna", "get_dna,regioned_dna-method" ] }, { "page": "get_du-methods", "title": "Get dinucleotide usage matrix", "topics": [ "get_du", "get_du,DNAStringSet-method", "get_du,regioned_dna-method" ] }, { "page": "get_freq-methods", "title": "Get codon usage frequency of synonymous codons", "topics": [ "get_freq", "get_freq,DNAStringSet-method", "get_freq,matrix-method", "get_freq,regioned_dna-method", "get_freq,vector-method" ] }, { "page": "get_nu-methods", "title": "Get nucleotide usage matrix", "topics": [ "get_nu", "get_nu,DNAStringSet-method", "get_nu,regioned_dna-method" ] }, { "page": "get_region-methods", "title": "Get the variable region", "topics": [ "get_region", "get_region,regioned_dna-method" ] }, { "page": "get_rscu-methods", "title": "Get Relative Synonymous Codon Usage (rscu) of synonymous codons", "topics": [ "get_rscu", "get_rscu,DNAStringSet-method", "get_rscu,regioned_dna-method" ] }, { "page": "input_seq-methods", "title": "Import region / constructing regioned_dna object", "topics": [ "input_seq", "input_seq,character-method", "input_seq,DNAString-method", "input_seq,DNAStringSet-method" ] }, { "page": "regioned_dna-class", "title": "An S4 class to record DNA sequences and variable regions for mutations", "topics": [ "regioned_dna-class" ] }, { "page": "seq_random-methods", "title": "Generate 'n' random DNA sequnces of length 'm'", "topics": [ "seq_random", "seq_random,numeric,numeric-method" ] } ], "_readme": "https://github.com/bioc/SynMut/raw/HEAD/README.md", "_rundeps": [ "ade4", "BiocGenerics", "Biostrings", "cli", "crayon", "generics", "glue", "IRanges", "lattice", "lifecycle", "magrittr", "MASS", "nlme", "pixmap", "Rcpp", "RcppArmadillo", "rlang", "S4Vectors", "segmented", "Seqinfo", "seqinr", "sp", "stringi", "stringr", "vctrs", "XVector" ], "_vignettes": [ { "source": "SynMut.Rmd", "filename": "SynMut.html", "title": "SynMut: Tools for Designing Synonymously Mutated Sequences", "author": "Haogao Gu, Leo L.M. Poon, School of Public Health, The University of Hong Kong", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Getting started", "Installation", "Input data", "Access the data", "Generating mutations", "Random synonymous mutants", "Synonymous mutants with maximal/minimal usage of specific codon", "Synonymous mutants with maximal/minimal usage of specific dinucleotide", "Synonymous mutants mimicking a specific codon usage pattern", "Output the results", "Session information" ], "created": "2019-04-23 08:43:34", "modified": "2019-04-29 07:33:48", "commits": 5 } ], "_score": 4.301029995663981, "_indexed": true, "_nocasepkg": "synmut", "_universes": [ "bioc", "koohoko" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.29.0", "date": "2026-07-09T09:59:41.000Z", "distro": "resolute", "commit": "b50cc017ecd70430ec65a7ba695a5aeecfe5419b", "fileid": "https://r2.ropensci.org/e54933efd5f046c6ef75c1792a4e80c860af6798105287a122d5b75dfd9c7a80", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29009679252" }, { "r": "4.6.1", "os": "linux", "version": "1.29.0", "date": "2026-07-09T09:59:35.000Z", "distro": "resolute", "commit": "b50cc017ecd70430ec65a7ba695a5aeecfe5419b", "fileid": "https://r2.ropensci.org/1999ed3dd744e8246cf7e69a69375524e3ed42c18770065a14a49134827178bd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29009679252" }, { "r": "4.5.3", "os": "mac", "version": "1.29.0", "date": "2026-07-09T09:57:35.000Z", "commit": "b50cc017ecd70430ec65a7ba695a5aeecfe5419b", "fileid": "https://r2.ropensci.org/6f93111fe00a96613cd13502fbd5c50c338e2fb615aacce48da07ba0c4dd9391", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29009679252" }, { "r": "4.6.1", "os": "mac", "version": "1.29.0", "date": "2026-07-09T09:57:41.000Z", "commit": "b50cc017ecd70430ec65a7ba695a5aeecfe5419b", "fileid": "https://r2.ropensci.org/f7313c6743a40c4608518b4b8c18dce7a7b3db6ce95a637f393617818ccf9a02", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29009679252" }, { "r": "4.6.0", "os": "wasm", "version": "1.29.0", "date": "2026-07-09T09:58:32.000Z", "commit": "b50cc017ecd70430ec65a7ba695a5aeecfe5419b", "fileid": "https://r2.ropensci.org/48aaf3d895169aa0bf3f8e830e6ffe2ac5442c53ccc8993fb9dfd51e7dfb6c91", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29009679252" }, { "r": "4.7.0", "os": "win", "version": "1.29.0", "date": "2026-07-09T09:57:43.000Z", "commit": "b50cc017ecd70430ec65a7ba695a5aeecfe5419b", "fileid": "https://r2.ropensci.org/bcf41842822a33185a2fefe870d422c8c33631bebfa3de494701394e6789dd4a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29009679252" }, { "r": "4.5.3", "os": "win", "version": "1.29.0", "date": "2026-07-09T09:58:01.000Z", "commit": "b50cc017ecd70430ec65a7ba695a5aeecfe5419b", "fileid": "https://r2.ropensci.org/05af5ff3b8e1c29abf9f05079e120a75d88923956eb9f5f5582ffdf85fac72d5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29009679252" }, { "r": "4.6.1", "os": "win", "version": "1.29.0", "date": "2026-07-09T09:57:48.000Z", "commit": "b50cc017ecd70430ec65a7ba695a5aeecfe5419b", "fileid": "https://r2.ropensci.org/0bd8988810e5be92cabfe753566c93d5dd8cf14d29fd69e3cabe375ab1f81883", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29009679252" } ] }