Compute the automorphisms between DNA's Abelian group representations

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Documentation for package ‘GenomAutomorphism’ version 1.1.2

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aaindex2 List of 94 Amino Acid Matrices from AAindex
aaindex3 Statistical protein contact potentials matrices from AAindex ver.9.2
aa_mutmat Amino acid mutation matrix
aln Simulated 'DNAStringSet' class object
aminoacid_dist Distance Between Aminoacids in Terms of Codon Distance
aminoacid_dist-method Distance Between Aminoacids in Terms of Codon Distance
as.AutomorphismList Methods for AutomorphismList-class Objects
as.AutomorphismList-method Methods for AutomorphismList-class Objects
aut3D Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z5^3.
autby_coef Automorphisms between DNA Primate BRCA1 Genes Grouped by Coefficients
autm Automorphisms between DNA Sequences from two COVID-19 genomes
autm_3d Automorphisms between DNA Sequences from two COVID-19 genomes
autm_z125 Automorphisms between DNA Sequences from two COVID-19 genomes
automorphismByRanges Get the automorphisms by ranges.
automorphismByRanges-method Get the automorphisms by ranges.
automorphisms Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in a Given Abelian group.
automorphisms-method Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in a Given Abelian group.
automorphism_bycoef Autmorphism Grouping by Coefficient
automorphism_bycoef-method Autmorphism Grouping by Coefficient
autZ125 Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z125.
autZ5 Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z5.
autZ64 Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z64.
base2codon Split a DNA sequence into codons
base2codon-method Split a DNA sequence into codons
base2int Replace bases with integers from Z4 and Z5
base2int-method Replace bases with integers from Z4 and Z5
base_coord Base coordinates on a given a given Abelian group representation.
base_coord-method Base coordinates on a given a given Abelian group representation.
brca1_aln Multiple Sequence Alignment (MSA) of Primate BRCA1 DNA repair genes.
brca1_aln2 Multiple Sequence Alignment (MSA) of Primate BRCA1 DNA repair genes.
brca1_autm Automorphisms between DNA Sequences from Primate BRCA1 Genes
brca1_autm2 Automorphisms between DNA Sequences from Primate BRCA1 Genes
cdm_z64 Codon Distance Matrices for the Standard Genetic Code on Z4
codon_coord Codon coordinates on a given a given Abelian group representation.
codon_coord-method Codon coordinates on a given a given Abelian group representation.
codon_dist Weighted Manhattan Distance Between Codons
codon_dist-method Weighted Manhattan Distance Between Codons
codon_dist_matrix Compute Codon Distance Matrix
conserved_regions Conserved and Non-conserved Regions from a MSA
conserved_regions-method Conserved and Non-conserved Regions from a MSA
covid_aln Pairwise Sequence Alignment (MSA) of COVID-19 genomes.
covid_autm Automorphisms between DNA Sequences from two COVID-19 genomes
cyc_aln Multiple Sequence Alignment (MSA) of Primate Somatic Cytochrome C
cyc_autm Automorphisms between DNA Sequences from Primate Cytochrome C Genes
GenomAutomorphism GenomAutomorphism: An R package to compute the automorphisms between DNA sequences represented as elements from an Abelian group.
getAutomorphisms Get Automorphisms
getAutomorphisms-method Get Automorphisms
get_coord DNA base/codon sequence and coordinates represented on a given Abelian group.
get_coord-method DNA base/codon sequence and coordinates represented on a given Abelian group.
get_mutscore Get Mutation Score from an AAindex Matrix
get_mutscore-method Get Mutation Score from an AAindex Matrix
matrices Get the Coordinate Representation from DNA Sequences on Specified Abelian Group
matrices-method Get the Coordinate Representation from DNA Sequences on Specified Abelian Group
mut_type Classification of DNA base mutations
seqranges Get DNA sequence Ranges and Coordinates representation on a given Abelian Group
seqranges-method Get DNA sequence Ranges and Coordinates representation on a given Abelian Group
slapply Apply a function over a list-like object preserving its attributes
sortByChromAndEnd Sorting 'GRanges-class' objects
sortByChromAndStart Sorting 'GRanges-class' objects
str2chr String to Character
str2chr-method String to Character
str2dig String to Digits
str2dig-method String to Digits
translation Translation of DNA/RNA sequences
translation-method Translation of DNA/RNA sequences