Package: GenomAutomorphism 1.7.0

Robersy Sanchez

GenomAutomorphism: Compute the automorphisms between DNA's Abelian group representations

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.

Authors:Robersy Sanchez [aut, cre]

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Bug tracker:https://github.com/genomaths/genomautomorphism/issues

On BioConductor:GenomAutomorphism-1.7.0(bioc 3.20)GenomAutomorphism-1.6.0(bioc 3.19)

bioconductor-package

80 exports 0.49 score 49 dependencies

Last updated 2 months agofrom:2ab18e54a1

Exports:aa_indexaa_mutmataa_phychem_indexAAMultipleAlignmentAAStringSetaminoacid_distas.AutomorphismListas.listaut3Dautomorphism_bycoefautomorphismByRangesautomorphismsautZ125autZ5autZ64base_coordbase_matrixbase_seq2string_setbase2codonbase2intcodon_coordcodon_distcodon_dist_matrixcodon_matrixCodonMatrixcolMeans2colSdscolSums2colVarsconserved_regionscoordListdna_phychemDNAMultipleAlignmentDNAStringSetendend<-GENETIC_CODE_TABLEget_coordget_mutscoregetAutomorphismsgetGeneticCodeGRangesListGRangesMatrixSeqListCodonMatrixmakeGRangesFromDataFramematricesMatrixSeqmcolsmcols<-modmodeqmodlinmodlineqmodqmut_typepeptide_phychem_indexreadDNAMultipleAlignmentrowMeans2rowSdsrowSums2rowVarsseq2grangesseqrangesseqRangessetValidity2showslapplysortByChromAndEndsortByChromAndStartstartstart<-str2chrstr2digstrandstrand<-subseqtranslatetranslationunmaskedwidth

Dependencies:askpassBHBiocGenericsBiocParallelBiostringsclicodetoolscpp11crayoncurldata.tabledoParalleldplyrfansiforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesiteratorsjsonlitelambda.rlifecyclemagrittrmatrixStatsmimenumbersopensslpillarpkgconfigR6rlangS4VectorssnowsystibbletidyselectUCSC.utilsutf8vctrswithrXVectorzlibbioc