{ "_id": "6abe165d99f7aa8c6aa51d6b", "Package": "GenomAutomorphism", "Title": "Compute the automorphisms between DNA's Abelian group\nrepresentations", "Version": "1.15.2", "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", "Collate": "'GenomAutomorphism.R' 'aa_phychem_index.R' 'allClasses.R'\n'aminoacid_dist.R' 'as.AutomorphismList.R' 'aut3D.R'\n'autZ125.R' 'autZ5.R' 'autZ64.R' 'automorphismByRanges.R'\n'automorphism_bycoef.R' 'automorphism_prob.R' 'automorphisms.R'\n'base2codon.R' 'base2int.R' 'base_methods.R' 'codon_coord.R'\n'codon_dist.R' 'codon_dist_matrix.R' 'codon_matrix.R'\n'conserved_regions.R' 'data_aaindex1.R' 'data_aaindex2.R'\n'data_aaindex3.R' 'data_aln.R' 'data_autby_coef.R'\n'data_autm.R' 'data_autm_3d.R' 'data_autm_z125.R'\n'data_brca1_aln.R' 'data_brca1_aln2.R' 'data_brca1_autm.R'\n'data_brca1_autm2.R' 'data_cdm_z64.R' 'data_covid_aln.R'\n'data_covid_autm.R' 'data_cyc_aln.R' 'data_cyc_autm.R'\n'data_dna_phyche.R' 'dna_phychem.R' 'extract-methods.R'\n'getAutomorphisms.R' 'get_coord.R' 'get_mutscore.R'\n'matrices.R' 'mod.R' 'modeq.R' 'modlineq.R' 'mut_type.R'\n'peptide_phychem_index.R' 'reexport.R' 'seqranges.R'\n'show-methods.R' 'slapply.R' 'sortByChromAndStart.R'\n'str2chr.R' 'str2dig.R' 'translation.R'\n'MultipleAlignment-methods.R'", "Roxygen": "list(markdown = TRUE)", "Language": "en-US", "LazyData": "false", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.0.0", "RoxygenNote": "8.0.0", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-08-02 02:13:51 UTC", "RemoteUrl": "https://github.com/bioc/GenomAutomorphism", "RemoteRef": "HEAD", "RemoteSha": "412dbaa9ea6a634c5895f6328dbacf5abe82bab2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-01 08:05:53 UTC", "User": "root" }, "Author": "Robersy Sanchez [aut, cre] (ORCID:\n)", "Maintainer": "Robersy Sanchez ", "_user": "bioc", "_type": "src", "_file": "GenomAutomorphism_1.15.2.tar.gz", "_fileid": "https://r2.ropensci.org/9d54e81bdeb2a947e914bb90aa4ceed2a658c8fd553136c99b9cdb68db96127c", "_filesize": 1469443, "_sha256": "9d54e81bdeb2a947e914bb90aa4ceed2a658c8fd553136c99b9cdb68db96127c", "_expires": "2027-01-09T08:14:19.000Z", "_created": "2026-10-01T08:05:53.000Z", "_published": "2026-10-01T08:14:21.237Z", "_bioccheck": { "error": 0, "warning": 0, "note": 2 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/36833784332", "_status": "success", "_upstream": "https://github.com/bioc/GenomAutomorphism", "_commit": { "id": "412dbaa9ea6a634c5895f6328dbacf5abe82bab2", "author": "genomaths ", "committer": "genomaths ", "message": "Fix Bioconductor devel build failure from Biostrings >= 2.81.3 (Bioconductor 3.24).\n", "time": 1785636831 }, "_maintainer": { "name": "Robersy Sanchez", "email": "genomicmath@gmail.com", "login": "genomaths", "twitter": "@robersysr", "description": "Mathematical Biologist", "uuid": 18340747, "orcid": "0000-0002-5246-1453" }, "_distro": "resolute", "_jobs": [ { "job": 110277883753, "time": 185, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11148138678" }, { "job": 110277883774, "time": 345, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11147404914" }, { "job": 110277883711, "time": 368, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11147544667" }, { "job": 110277883840, "time": 224, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11149140092" }, { "job": 110277883688, "time": 200, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11148616538" }, { "job": 110276292379, "time": 290, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11148835142" }, { "job": 110277883794, "time": 154, "config": 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] }, { "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 \\mathbb{Z}_5^3.", "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": "Automorphism Grouping by Coefficient", "topics": [ "automorphism_bycoef", "automorphism_bycoef,Automorphism-method", "automorphism_bycoef,AutomorphismList-method" ] }, { "page": "automorphism_prob", "title": "Automorphism 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,DNAMultipleAlignment-method", "automorphisms,DNAStringSet_OR_NULL-method" ] }, { "page": "autZ125", "title": "Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in \\mathbb{Z}_{125}.", "topics": [ "autZ125" ] }, { "page": "autZ5", "title": "Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in \\mathbb{Z}_5.", "topics": [ "autZ5" ] }, { "page": "autZ64", "title": "Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in \\mathbb{Z}_{64}.", "topics": [ "autZ64" ] }, { "page": "base_methods", "title": "DNA Sequences Methods", "topics": [ "base_coord", "base_coord,DNAMultipleAlignment-method", "base_coord,DNAStringSet_OR_NULL-method", "base_matrix", "base_matrix,DNAMultipleAlignment-method", "base_matrix,DNAStringSet_OR_NULL-method", "base_methods", "base_seq2string_set", "base_seq2string_set,BaseSeq-method", "seq2granges", "seq2granges,DNAMultipleAlignment-method", "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 \\mathbb{Z}_4 and \\mathbb{Z}_5", "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 \\mathbb{Z}_4", "topics": [ "cdm_z64" ] }, { "page": "codon_coord", "title": "Codon coordinates on a given Abelian group representation.", "topics": [ "codon_coord", "codon_coord,BaseGroup-method", "codon_coord,DNAMultipleAlignment-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 an 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,DNAMultipleAlignment-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,DNAMultipleAlignment-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,DNAMultipleAlignment-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", 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