'%%' | Modulo Operation |
aaindex1 | List of 571 Amino Acid Physicochemical Indexes from AAindex Database |
aaindex2 | List of 94 Amino Acid Matrices from AAindex |
aaindex3 | Statistical protein contact potentials matrices from AAindex ver.9.2 |
aa_index | Amino acid mutation matrix |
aa_mutmat | Amino acid mutation matrix |
aa_phychem_index | 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 | DNA Sequences Methods |
base_coord-method | DNA Sequences Methods |
base_matrix | DNA Sequences Methods |
base_matrix-method | DNA Sequences Methods |
base_methods | DNA Sequences Methods |
base_seq2string_set | DNA Sequences Methods |
base_seq2string_set-method | DNA Sequences Methods |
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 |
codon_matrix | Codon Coordinate Matrix |
codon_matrix-method | Codon Coordinate 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 |
dna_phyche | Some Physicochemical Properties of DNA bases |
dna_phychem | DNA numerical matrix |
dna_phychem-method | DNA numerical matrix |
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 or a Mutation/Distance Matrix |
get_mutscore-method | Get Mutation Score from an AAindex or a Mutation/Distance 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 |
mod | Modulo Operation |
mod-method | Modulo Operation |
modlineq | Modular System of Linear Equation Solver (MLE) |
modulo | Modulo Operation |
mut_type | Classification of DNA base mutations |
peptide_phychem_index | Amino acid numerical matrix |
peptide_phychem_index-method | Amino acid numerical matrix |
seq2granges | DNA Sequences Methods |
seq2granges-method | DNA Sequences Methods |
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 |