Man pages for genomaths/GenomAutomorphism
Compute the automorphisms between DNA's Abelian group representations
| aaindex1 | List of 571 Amino Acid Physicochemical Indexes from AAindex... |
| aaindex2 | List of 94 Amino Acid Matrices from AAindex |
| aaindex3 | Statistical protein contact potentials matrices from AAindex... |
| aa_phychem_index | Amino acid mutation matrix |
| aln | Simulated 'DNAStringSet' class object |
| aminoacid_dist | Distance Between Aminoacids in Terms of Codon Distance |
| as.AutomorphismList | Methods for AutomorphismList-class Objects |
| aut3D | Compute the Automorphisms of Mutational Events Between two... |
| autby_coef | Automorphisms between DNA Primate BRCA1 Genes Grouped by... |
| 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 |
| Automorphism | A class definition to store codon automorphisms in a given... |
| automorphism_bycoef | Autmorphism Grouping by Coefficient |
| AutomorphismByCoef | A class definition to store conserved gene/genomic regions... |
| AutomorphismByCoefList | A class definition for a list of AutomorphismByCoef class... |
| automorphismByRanges | Get the automorphisms by ranges. |
| AutomorphismList | A class definition to store list of Automorphism class... |
| automorphism_prob | Autmorphism Probability |
| automorphisms | Compute the Automorphisms of Mutational Events Between two... |
| autZ125 | Compute the Automorphisms of Mutational Events Between two... |
| autZ5 | Compute the Automorphisms of Mutational Events Between two... |
| autZ64 | Compute the Automorphisms of Mutational Events Between two... |
| base2codon | Split a DNA sequence into codons |
| base2int | Replace bases with integers from Z4 and Z5 |
| BaseGroup | A class definition to store codon automorphisms in given in... |
| BaseGroup_OR_CodonGroup | A definition for the union of classes 'BaseGroup' and... |
| base_methods | DNA Sequences Methods |
| base_repl | Replace bases with integers |
| BaseSeq | A class definition to store DNA base sequence. |
| BaseSeqMatrix | A class definition to Store DNA base sequence coordinates in... |
| brca1_aln | Multiple Sequence Alignment (MSA) of Primate BRCA1 DNA repair... |
| brca1_aln2 | Multiple Sequence Alignment (MSA) of Primate BRCA1 DNA repair... |
| 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... |
| codon_dist | Weighted Manhattan Distance Between Codons |
| codon_dist_matrix | Compute Codon Distance Matrix |
| CodonGroup | A class definition to store codon automorphisms in given in... |
| codon_matrix | Codon Coordinate Matrix |
| CodonMatrix | A Convenient Class to Store a Codon Coordinate in given... |
| CodonSeq | A class definition to store codon coordinates given in the... |
| ConservedRegion | A class definition to store conserved gene/genomic regions... |
| conserved_regions | 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... |
| cyc_autm | Automorphisms between DNA Sequences from Primate Cytochrome C... |
| dna_phyche | Some Physicochemical Properties of DNA bases |
| dna_phychem | DNA numerical matrix |
| extract-methods | An S4 class to extract elements for objects created with... |
| GenomAutomorphism | GenomAutomorphism: An R package to compute the automorphisms... |
| getAutomorphisms | Get Automorphisms |
| get_coord | DNA base/codon sequence and coordinates represented on a... |
| get_mutscore | Get Mutation Score from an AAindex or a Mutation/Distance... |
| GRangesMatrixSeq | Definition of GRangesMatrixSeq-class |
| GRanges_OR_NULL | A definition for the union of 'GRanges' and 'NULL' class. |
| is.url | Check URLs |
| ListCodonMatrix | A Convenient Class to Store Codon Coordinates in given... |
| matrices | Get the Coordinate Representation from DNA Sequences on... |
| MatrixList | Definition of MatrixList-class |
| MatrixSeq | Definition of MatrixSeq-class |
| mod | Modulo Operation |
| modeq | A Wrapper Calling Modular Linear Equation Solver (MLE) |
| modlineq | Modular System of Linear Equation Solver (MLE) |
| mut_type | Classification of DNA base mutations |
| peptide_phychem_index | Amino acid numerical matrix |
| reexports | Reexport useful functions to be available to users |
| seqranges | Get DNA sequence Ranges and Coordinates representation on a... |
| show-methods | Show method for 'CodonSeq' class object |
| slapply | Apply a function over a list-like object preserving its... |
| sortByChromAndStart | Sorting 'GRanges-class' objects |
| str2chr | String to Character |
| str2dig | String to Digits |
| translation | Translation of DNA/RNA sequences |
| valid.Automorphism | Valid Automorphism mcols |
| valid.AutomorphismByCoef | Valid AutomorphismByCoef mcols |
| valid.AutomorphismByCoefList | Valid AutomorphismByCoefList mcols |
| valid.AutomorphismList | Valid AutomorphismList mcols |
| valid.BaseGroup | Valid BaseGroup mcols |
| valid.CodonGroup | Valid CodonGroup mcols |
| valid.MatrixList | Valid MatrixList |
