{ "_id": "6a1acf0f1d7bb097a09e0446", "Package": "GenomAutomorphism", "Title": "Compute the automorphisms between DNA's Abelian group\nrepresentations", "Version": "1.15.0", "Authors@R": "person( given = \"Robersy\",\nfamily = \"Sanchez\",\nrole = c(\"aut\", \"cre\"),\nemail = \"genomicmath@gmail.com\",\ncomment = c(ORCID = \"0000-0002-5246-1453\"))", "URL": "https://github.com/genomaths/GenomAutomorphism", "BugReports": "https://github.com/genomaths/GenomAutomorphism/issues", "Description": "This is a R package to compute the automorphisms between\npairwise aligned DNA sequences represented as elements from a\nGenomic Abelian group. In a general scenario, from genomic\nregions till the whole genomes from a given population (from\nany species or close related species) can be algebraically\nrepresented as a direct sum of cyclic groups or more\nspecifically Abelian p-groups. Basically, we propose the\nrepresentation of multiple sequence alignments of length N bp\nas element of a finite Abelian group created by the direct sum\nof homocyclic Abelian group of prime-power order.", "License": "Artistic-2.0", "Encoding": "UTF-8", "biocViews": "MathematicalBiology, ComparativeGenomics,\nFunctionalGenomics, MultipleSequenceAlignment, WholeGenome", "RoxygenNote": "7.3.2", "Roxygen": "list(markdown = TRUE)", "Language": "en-US", "LazyData": "false", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:58:46 UTC", "RemoteUrl": "https://github.com/bioc/GenomAutomorphism", "RemoteRef": "HEAD", "RemoteSha": "34d8013455723cf11bc1b6c548fefc8e46ee9b8d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:14:35 UTC", "User": "root" }, "Author": "Robersy Sanchez [aut, cre] (ORCID:\n)", "Maintainer": "Robersy Sanchez ", "MD5sum": "6dba453981c43b560ca77e48f32b08a9", "_user": "bioc", "_type": "src", "_file": "GenomAutomorphism_1.15.0.tar.gz", "_fileid": "9b3781052517d2cbf7e15c474737b7862ab5a3a1f17c65de79e8f05bc085f7eb", "_filesize": 1578412, "_sha256": "9b3781052517d2cbf7e15c474737b7862ab5a3a1f17c65de79e8f05bc085f7eb", "_created": "2026-05-30T08:14:35.000Z", "_published": "2026-05-30T11:50:39.105Z", "_jobs": [ { "job": 78635911784, "time": 173, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7306767422" }, { "job": 78635911781, "time": 357, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7306784382" }, { "job": 78635911803, "time": 290, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7306778035" }, { "job": 78635911793, "time": 208, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7307961466" }, { "job": 78635911794, "time": 234, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", 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"bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381126 }, "_maintainer": { "name": "Robersy Sanchez", "email": "genomicmath@gmail.com", "login": "genomaths", "twitter": "@robersysr", "description": "Mathematical Biologist", "uuid": 18340747, "orcid": "0000-0002-5246-1453" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "Biostrings", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "XVector", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "doParallel", "role": 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], "fields": [], "table": true, "tojson": true }, { "name": "covid_aln", "title": "Pairwise Sequence Alignment (MSA) of COVID-19 genomes.", "object": "covid_aln", "file": "covid_aln.rda", "class": [ "DNAMultipleAlignment" ], "fields": [], "table": false, "tojson": false }, { "name": "covid_autm", "title": "Automorphisms between DNA Sequences from two COVID-19 genomes", "object": "covid_autm", "file": "covid_autm.rda", "class": [ "Automorphism" ], "fields": [], "table": false, "tojson": false }, { "name": "cyc_aln", "title": "Multiple Sequence Alignment (MSA) of Primate Somatic Cytochrome C", "object": "cyc_aln", "file": "cyc_aln.rda", "class": [ "DNAMultipleAlignment" ], "fields": [], "table": false, "tojson": false }, { "name": "cyc_autm", "title": "Automorphisms between DNA Sequences from Primate Cytochrome C Genes", "object": "cyc_autm", "file": "cyc_autm.rda", "class": [ "AutomorphismList" ], "fields": [], "table": false, "tojson": false }, { "name": "dna_phyche", "title": "Some Physicochemical Properties of DNA bases", "object": "dna_phyche", "file": "dna_phyche.rda", "class": [ "data.frame" ], "fields": [ "proton_affinity", "partition_coef", "dipole_moment", "tautomerization_energy" ], "rows": 4, "table": true, "tojson": true } ], "_help": [ { "page": "aa_phychem_index", "title": "Amino acid mutation matrix", "topics": [ "aa_index", "aa_mutmat", "aa_phychem_index" ] }, { "page": "aaindex1", "title": "List of 571 Amino Acid Physicochemical Indexes from AAindex Database", "topics": [ "aaindex1" ] }, { "page": "aaindex2", "title": "List of 94 Amino Acid Matrices from AAindex", "topics": [ "aaindex2" ] }, { "page": "aaindex3", "title": "Statistical protein contact potentials matrices from AAindex ver.9.2", "topics": [ "aaindex3" ] }, { "page": "aln", "title": "Simulated 'DNAStringSet' class object", "topics": [ "aln" ] }, { "page": "aminoacid_dist", "title": "Distance Between Aminoacids in Terms of Codon Distance", "topics": [ "aminoacid_dist", "aminoacid_dist,AAStringSet,ANY-method", "aminoacid_dist,character,character-method", "aminoacid_dist,CodonGroup_OR_Automorphisms,ANY-method", "aminoacid_dist,DNAStringSet,ANY-method" ] }, { "page": "as.AutomorphismList", "title": "Methods for AutomorphismList-class Objects", "topics": [ "as.AutomorphismList", "as.AutomorphismList,GRangesList,GRanges_OR_NULL-method", "as.AutomorphismList,list,GRanges_OR_NULL-method" ] }, { "page": "aut3D", "title": "Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z5^3.", "topics": [ "aut3D" ] }, { "page": "autby_coef", "title": "Automorphisms between DNA Primate BRCA1 Genes Grouped by Coefficients", "topics": [ "autby_coef" ] }, { "page": "autm", "title": "Automorphisms between DNA Sequences from two COVID-19 genomes", "topics": [ "autm" ] }, { "page": "autm_3d", "title": "Automorphisms between DNA Sequences from two COVID-19 genomes", "topics": [ "autm_3d" ] }, { "page": "autm_z125", "title": "Automorphisms between DNA Sequences from two COVID-19 genomes", "topics": [ "autm_z125" ] }, { "page": "automorphism_bycoef", "title": "Autmorphism Grouping by Coefficient", "topics": [ "automorphism_bycoef", "automorphism_bycoef,Automorphism-method", "automorphism_bycoef,AutomorphismList-method" ] }, { "page": "automorphism_prob", "title": "Autmorphism Probability", "topics": [ "automorphism_prob", "automorphism_prob,AutomorphismByCoef-method", "automorphism_prob,AutomorphismByCoefList-method" ] }, { "page": "automorphismByRanges", "title": "Get the automorphisms by ranges.", "topics": [ "automorphismByRanges", "automorphismByRanges,Automorphism-method", "automorphismByRanges,AutomorphismList-method" ] }, { "page": "automorphisms", "title": "Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in a Given Abelian group.", "topics": [ "automorphisms", "automorphisms,DNAStringSet_OR_NULL-method" ] }, { "page": "autZ125", "title": "Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z125.", "topics": [ "autZ125" ] }, { "page": "autZ5", "title": "Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z5.", "topics": [ "autZ5" ] }, { "page": "autZ64", "title": "Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z64.", "topics": [ "autZ64" ] }, { "page": "base_methods", "title": "DNA Sequences Methods", "topics": [ "base_coord", "base_coord,DNAStringSet_OR_NULL-method", "base_matrix", "base_matrix,DNAStringSet_OR_NULL-method", "base_methods", "base_seq2string_set", "base_seq2string_set,BaseSeq-method", "seq2granges", "seq2granges,DNAStringSet_OR_NULL-method" ] }, { "page": "base2codon", "title": "Split a DNA sequence into codons", "topics": [ "base2codon", "base2codon,character-method", "base2codon,DNAMultipleAlignment-method", "base2codon,DNAStringSet-method" ] }, { "page": "base2int", "title": "Replace bases with integers from Z4 and Z5", "topics": [ "base2int", "base2int,character-method", "base2int,data.frame-method" ] }, { "page": "brca1_aln", "title": "Multiple Sequence Alignment (MSA) of Primate BRCA1 DNA repair genes.", "topics": [ "brca1_aln" ] }, { "page": "brca1_aln2", "title": "Multiple Sequence Alignment (MSA) of Primate BRCA1 DNA repair genes.", "topics": [ "brca1_aln2" ] }, { "page": "brca1_autm", "title": "Automorphisms between DNA Sequences from Primate BRCA1 Genes", "topics": [ "brca1_autm" ] }, { "page": "brca1_autm2", "title": "Automorphisms between DNA Sequences from Primate BRCA1 Genes", "topics": [ "brca1_autm2" ] }, { "page": "cdm_z64", "title": "Codon Distance Matrices for the Standard Genetic Code on Z4", "topics": [ "cdm_z64" ] }, { "page": "codon_coord", "title": "Codon coordinates on a given a given Abelian group representation.", "topics": [ "codon_coord", "codon_coord,BaseGroup-method", "codon_coord,DNAStringSet_OR_NULL-method", "codon_coord,matrix_OR_data_frame-method" ] }, { "page": "codon_dist", "title": "Weighted Manhattan Distance Between Codons", "topics": [ "codon_dist", "codon_dist,character-method", "codon_dist,CodonGroup_OR_Automorphisms-method", "codon_dist,DNAStringSet-method" ] }, { "page": "codon_dist_matrix", "title": "Compute Codon Distance Matrix", "topics": [ "codon_dist_matrix" ] }, { "page": "codon_matrix", "title": "Codon Coordinate Matrix", "topics": [ "codon_matrix", "codon_matrix,BaseSeqMatrix-method", "codon_matrix,DNAMultipleAlignment-method", "codon_matrix,DNAStringSet-method" ] }, { "page": "conserved_regions", "title": "Conserved and Non-conserved Regions from a MSA", "topics": [ "conserved_regions", "conserved_regions,Automorphism-method", "conserved_regions,AutomorphismByCoef-method", "conserved_regions,AutomorphismByCoefList-method", "conserved_regions,AutomorphismList-method" ] }, { "page": "covid_aln", "title": "Pairwise Sequence Alignment (MSA) of COVID-19 genomes.", "topics": [ "covid_aln" ] }, { "page": "covid_autm", "title": "Automorphisms between DNA Sequences from two COVID-19 genomes", "topics": [ "covid_autm" ] }, { "page": "cyc_aln", "title": "Multiple Sequence Alignment (MSA) of Primate Somatic Cytochrome C", "topics": [ "cyc_aln" ] }, { "page": "cyc_autm", "title": "Automorphisms between DNA Sequences from Primate Cytochrome C Genes", "topics": [ "cyc_autm" ] }, { "page": "dna_phyche", "title": "Some Physicochemical Properties of DNA bases", "topics": [ "dna_phyche" ] }, { "page": "dna_phychem", "title": "DNA numerical matrix", "topics": [ "dna_phychem", "dna_phychem,character-method", "dna_phychem,DNAStringSet_OR_DNAMultipleAlignment-method" ] }, { "page": "get_coord", "title": "DNA base/codon sequence and coordinates represented on a given Abelian group.", "topics": [ "get_coord", "get_coord,BaseGroup_OR_CodonGroup-method", "get_coord,DNAStringSet_OR_NULL-method" ] }, { "page": "get_mutscore", "title": "Get Mutation Score from an AAindex or a Mutation/Distance Matrix", "topics": [ "get_mutscore", "get_mutscore,BaseSeq,missing-method", "get_mutscore,character,character-method", "get_mutscore,DNAMultipleAlignment,missing-method", "get_mutscore,DNAStringSet,missing-method" ] }, { "page": "getAutomorphisms", "title": "Get Automorphisms", "topics": [ "getAutomorphisms", "getAutomorphisms,AutomorphismList-method", "getAutomorphisms,DataFrame_OR_data.frame-method", "getAutomorphisms,list-method" ] }, { "page": "matrices", "title": "Get the Coordinate Representation from DNA Sequences on Specified Abelian Group", "topics": [ "matrices", "matrices,CodonSeq-method", "matrices,DNAStringSet_OR_NULL-method", "matrices,MatrixList-method" ] }, { "page": "mod", "title": "Modulo Operation", "topics": [ "'%%'", "mod", "mod,matrix,numeric-method", "modulo" ] }, { "page": "modlineq", "title": "Modular System of Linear Equation Solver (MLE)", "topics": [ "modlineq" ] }, { "page": "mut_type", "title": "Classification of DNA base mutations", "topics": [ "mut_type" ] }, { "page": "peptide_phychem_index", "title": "Amino acid numerical matrix", "topics": [ "peptide_phychem_index", "peptide_phychem_index,character-method", "peptide_phychem_index,DNAStringSet_OR_DNAMultipleAlignment-method" ] }, { "page": "seqranges", "title": "Get DNA sequence Ranges and Coordinates representation on a given Abelian Group", "topics": [ "seqranges", "seqranges,CodonSeq-method", "seqranges,DNAStringSet_OR_NULL-method" ] }, { "page": "slapply", "title": "Apply a function over a list-like object preserving its attributes", "topics": [ "slapply" ] }, { "page": "sortByChromAndStart", "title": "Sorting 'GRanges-class' objects", "topics": [ "sortByChromAndEnd", "sortByChromAndStart" ] }, { "page": "str2chr", "title": "String to Character", "topics": [ "str2chr", "str2chr,character-method", "str2chr,list-method" ] }, { "page": "str2dig", "title": "String to Digits", "topics": [ "str2dig", "str2dig,character-method", "str2dig,list-method" ] }, { "page": "translation", "title": "Translation of DNA/RNA sequences", "topics": [ "translation", "translation,BioString-method", "translation,character-method" ] } ], "_pkglogo": "https://github.com/bioc/GenomAutomorphism/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/bioc/GenomAutomorphism/raw/HEAD/README.md", "_rundeps": [ "BH", "BiocGenerics", "BiocParallel", "Biostrings", "cli", "codetools", "cpp11", "crayon", "data.table", "doParallel", "dplyr", "foreach", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "glue", "IRanges", "iterators", "lambda.r", "lifecycle", "magrittr", "matrixStats", "numbers", "pillar", "pkgconfig", "R6", "rlang", "S4Vectors", "Seqinfo", "snow", "tibble", "tidyselect", "utf8", "vctrs", "withr", "XVector" ], "_vignettes": [ { "source": "GenomAutomorphism.Rmd", "filename": "GenomAutomorphism.html", "title": "Get started-with GenomAutomorphism", "author": "Robersy Sanchez", "engine": "knitr::rmarkdown", "headings": [ "GenomAutomorphism Overview", "Installing GenomAutomorphism", "Automorphisms", "Load the R libraries", "Read the alignment FASTA and encode the sequences", "Group representations", "\"Dual\" genetic-code cubes", "Automorphisms on $\\mathbb{Z}_{64}$", "Automorphisms between whole genomes of SARS-CoV-2 related coronaviruses", "Bar plot automorphism distribution by cubes", "Grouping automorphism by automorphism's coefficients. Types of mutations", "Conserved and non-conserved regions", "Conserved regions", "Automorphisms on $\\mathbb{Z}_{125}$", "Automorphisms on the Genetic-code Cube Representation on GF(5)", "Grouping automorphism by automorphism's coefficients", "References", "Session info" ], "created": "2021-10-24 03:26:05", "modified": "2025-07-23 00:06:38", "commits": 32 } ], "_score": 4.380211241711606, "_indexed": true, "_nocasepkg": "genomautomorphism", "_universes": [ "bioc", "genomaths" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.15.0", "date": "2026-05-30T08:18:16.000Z", "distro": "noble", "commit": "34d8013455723cf11bc1b6c548fefc8e46ee9b8d", "fileid": "1a6cdad6d4a34ffc2cfa436ee7cf9666952def96e30d89271d2b6809ea6ac0d6", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678896979" }, { "r": "4.6.0", "os": "linux", "version": "1.15.0", "date": "2026-05-30T08:17:39.000Z", "distro": "noble", "commit": "34d8013455723cf11bc1b6c548fefc8e46ee9b8d", "fileid": "d0b3a9fbf5906c00d6a1ba6a847d90a2b8a122ba72e4bf97dc49be003d22f4c9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678896979" }, { "r": "4.5.3", "os": "mac", "version": "1.15.0", "date": "2026-05-30T11:47:55.000Z", "commit": "34d8013455723cf11bc1b6c548fefc8e46ee9b8d", "fileid": "7b5437748709d378b0a78d2b4f99627951692c82e2141f34078545b50e1cd031", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678896979" }, { "r": "4.6.0", "os": "mac", "version": "1.15.0", "date": "2026-05-30T11:48:04.000Z", "commit": "34d8013455723cf11bc1b6c548fefc8e46ee9b8d", "fileid": "de2a831a2e7e4644e3b7ca403f472fdc61a9d61a1404786b790ba5e2090e4138", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678896979" }, { "r": "4.6.0", "os": "wasm", "version": "1.15.0", "date": "2026-05-30T08:17:29.000Z", "commit": "34d8013455723cf11bc1b6c548fefc8e46ee9b8d", "fileid": "7f9ff3bb5cf91700e406eb38add7c66b4dd29eb6372b2f8ae6488f4a3d58630d", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678896979" }, { "r": "4.7.0", "os": "win", "version": "1.15.0", "date": "2026-05-30T08:16:19.000Z", "commit": "34d8013455723cf11bc1b6c548fefc8e46ee9b8d", "fileid": "daa49eff99b6751b5c2f646bc773f8385d6486947073928d95ef6d8441b3b92c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678896979" }, { "r": "4.5.3", "os": "win", "version": "1.15.0", "date": "2026-05-30T08:17:18.000Z", "commit": "34d8013455723cf11bc1b6c548fefc8e46ee9b8d", "fileid": "6d710f66b5b0afc56025025e5642ddafbffba3761daa0f50387187293d192b7f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678896979" }, { "r": "4.6.0", "os": "win", "version": "1.15.0", "date": "2026-05-30T08:16:30.000Z", "commit": "34d8013455723cf11bc1b6c548fefc8e46ee9b8d", "fileid": "ae3402e2eb0294c861b2657d254b313a92bb82ac74e89999ab8be9b48de26894", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678896979" } ] }