Package: GenomAutomorphism
Title: Compute the automorphisms between DNA's Abelian group
        representations
Version: 1.15.2
Authors@R: 
    person( given = "Robersy",
            family = "Sanchez",
            role = c("aut", "cre"),
            email = "genomicmath@gmail.com",
            comment = 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
        pairwise aligned DNA sequences represented as elements from a
        Genomic Abelian group. In a general scenario, from genomic
        regions till the whole genomes from a given population (from
        any species or close related species) can be algebraically
        represented as a direct sum of cyclic groups or more
        specifically Abelian p-groups. Basically, we propose the
        representation of multiple sequence alignments of length N bp
        as element of a finite Abelian group created by the direct sum
        of homocyclic Abelian group of prime-power order.
Depends: R (>= 4.5.0),
License: Artistic-2.0
Encoding: UTF-8
biocViews: MathematicalBiology, ComparativeGenomics,
        FunctionalGenomics, MultipleSequenceAlignment, WholeGenome
Imports: Biostrings, MultipleAlignment, BiocGenerics, BiocParallel,
        Seqinfo, GenomicRanges, IRanges, matrixStats, XVector, dplyr,
        data.table, parallel, doParallel, foreach, methods, S4Vectors,
        stats, numbers, utils
Suggests: spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr
Collate: 'GenomAutomorphism.R' 'aa_phychem_index.R' 'allClasses.R'
        'aminoacid_dist.R' 'as.AutomorphismList.R' 'aut3D.R'
        'autZ125.R' 'autZ5.R' 'autZ64.R' 'automorphismByRanges.R'
        'automorphism_bycoef.R' 'automorphism_prob.R' 'automorphisms.R'
        'base2codon.R' 'base2int.R' 'base_methods.R' 'codon_coord.R'
        'codon_dist.R' 'codon_dist_matrix.R' 'codon_matrix.R'
        'conserved_regions.R' 'data_aaindex1.R' 'data_aaindex2.R'
        'data_aaindex3.R' 'data_aln.R' 'data_autby_coef.R'
        'data_autm.R' 'data_autm_3d.R' 'data_autm_z125.R'
        'data_brca1_aln.R' 'data_brca1_aln2.R' 'data_brca1_autm.R'
        'data_brca1_autm2.R' 'data_cdm_z64.R' 'data_covid_aln.R'
        'data_covid_autm.R' 'data_cyc_aln.R' 'data_cyc_autm.R'
        'data_dna_phyche.R' 'dna_phychem.R' 'extract-methods.R'
        'getAutomorphisms.R' 'get_coord.R' 'get_mutscore.R'
        'matrices.R' 'mod.R' 'modeq.R' 'modlineq.R' 'mut_type.R'
        'peptide_phychem_index.R' 'reexport.R' 'seqranges.R'
        'show-methods.R' 'slapply.R' 'sortByChromAndStart.R'
        'str2chr.R' 'str2dig.R' 'translation.R'
        '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: 2026-10-01 08:05:53 UTC; root
Author: Robersy Sanchez [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5246-1453>)
Maintainer: Robersy Sanchez <genomicmath@gmail.com>