genomaths/GenomAutomorphism
Compute the automorphisms between DNA's Abelian group representations

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Search the genomaths/GenomAutomorphism package
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genomaths/GenomAutomorphism: Compute the automorphisms between DNA's Abelian group representations
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API

API for genomaths/GenomAutomorphism
Compute the automorphisms between DNA's Abelian group representations

Global functions
$ Man page
$,AutomorphismList-method Man page
$,ListCodonMatrix-method Man page
$,MatrixSeq-method Man page
'%%' Man page
'[' Man page
'[[' Man page
'names<-' Man page
.showMatrix Source code
AAMultipleAlignment Man page
AAStringSet Man page
Automorphism Man page
Automorphism-class Man page
AutomorphismByCoef Man page
AutomorphismByCoef-class Man page
AutomorphismByCoefList Man page
AutomorphismByCoefList-class Man page
AutomorphismList Man page
AutomorphismList-class Man page
BaseGroup Man page
BaseGroup-class Man page
BaseGroup_OR_CodonGroup Man page
BaseGroup_OR_CodonGroup-class Man page
BaseSeq Man page
BaseSeq-class Man page
BaseSeqMatrix Man page
BaseSeqMatrix-class Man page
CodonCoordZ4toZ64 Source code
CodonCoordZ5toZ125 Source code
CodonGroup Man page
CodonGroup-class Man page
CodonMatrix Man page Source code
CodonMatrix-class Man page
CodonSeq Man page
CodonSeq-class Man page
ConservedRegion Man page
ConservedRegion-class Man page
ConservedRegionList Man page
ConservedRegionList-class Man page
DNAMultipleAlignment Man page
DNAStringSet Man page
DNAStringSet_OR_DNAMultipleAlignment-class Man page
DNAStringSet_OR_NULL-class Man page
DataFrame_OR_data.frame-class Man page
GENETIC_CODE_TABLE Man page
GRangesList Man page
GRangesMatrixSeq Man page Source code
GRangesMatrixSeq-class Man page
GRanges_OR_NULL-class Man page
GenomAutomorphism Man page
GenomAutomorphism-package Man page
ListCodonMatrix Man page Source code
ListCodonMatrix-class Man page
MatrixList Man page
MatrixList-class Man page
MatrixSeq Man page Source code
MatrixSeq-class Man page
[,AutomorphismList,ANY-method Man page
[,ListCodonMatrix,ANY-method Man page
[,MatrixSeq,ANY-method Man page
[[,AutomorphismList-method Man page
[[,ListCodonMatrix-method Man page
aa_index Man page Source code
aa_mutmat Man page Source code
aa_phychem_index Man page Source code
aaindex1 Man page
aaindex2 Man page
aaindex3 Man page
aln Man page
aminoacid_dist Man page
aminoacid_dist,AAStringSet,ANY-method Man page
aminoacid_dist,CodonGroup_OR_Automorphisms,ANY-method Man page
aminoacid_dist,DNAStringSet,ANY-method Man page
aminoacid_dist,character,character-method Man page
as.AutomorphismList Man page
as.AutomorphismList,GRangesList,GRanges_OR_NULL-method Man page
as.AutomorphismList,list,GRanges_OR_NULL-method Man page
as.list,AutomorphismList-method Man page
as_list_of_AutomorphismByCoef Source code
as_list_of_ConservedRegion Source code
aut3D Man page Source code
autZ125 Man page Source code
autZ5 Man page Source code
autZ64 Man page Source code
autby_coef Man page
autm Man page
autm_3d Man page
autm_z125 Man page
automorfismos Source code
automorfismos_3D Source code
automorfismos_Z125 Source code
automorfismos_Z5 Source code
automorphismByRanges Man page
automorphismByRanges,Automorphism-method Man page
automorphismByRanges,AutomorphismList-method Man page
automorphism_bycoef Man page
automorphism_bycoef,Automorphism-method Man page
automorphism_bycoef,AutomorphismList-method Man page
automorphism_prob Man page
automorphism_prob,AutomorphismByCoef-method Man page
automorphism_prob,AutomorphismByCoefList-method Man page
automorphisms Man page
automorphisms,DNAStringSet_OR_NULL-method Man page
base2codon Man page
base2codon,DNAMultipleAlignment-method Man page
base2codon,DNAStringSet-method Man page
base2codon,character-method Man page
base2int Man page
base2int,character-method Man page
base2int,data.frame-method Man page
base_coord Man page
base_coord,DNAStringSet_OR_NULL-method Man page
base_matrix Man page
base_matrix,DNAStringSet_OR_NULL-method Man page
base_methods Man page
base_repl Man page Source code
base_seq2string_set Man page
base_seq2string_set,BaseSeq-method Man page
brca1_aln Man page
brca1_aln2 Man page
brca1_autm Man page
brca1_autm2 Man page
cdm_z64 Man page
codon_coord Man page
codon_coord,BaseGroup-method Man page
codon_coord,DNAStringSet_OR_NULL-method Man page
codon_coord,matrix_OR_data_frame-method Man page
codon_dist Man page
codon_dist,CodonGroup_OR_Automorphisms-method Man page
codon_dist,DNAStringSet-method Man page
codon_dist,character-method Man page
codon_dist_matrix Man page Source code
codon_matrix Man page
codon_matrix,BaseSeqMatrix-method Man page
codon_matrix,DNAMultipleAlignment-method Man page
codon_matrix,DNAStringSet-method Man page
colMeans2 Man page
colSds Man page
colSums2 Man page
colVars Man page
conserved_regions Man page
conserved_regions,Automorphism-method Man page
conserved_regions,AutomorphismByCoef-method Man page
conserved_regions,AutomorphismByCoefList-method Man page
conserved_regions,AutomorphismList-method Man page
coordList Man page
coordList,CodonSeq-method Man page
covid_aln Man page
covid_autm Man page
cyc_aln Man page
cyc_autm Man page
digit_rep Source code
dna_phyche Man page
dna_phychem Man page
dna_phychem,DNAStringSet_OR_DNAMultipleAlignment-method Man page
dna_phychem,character-method Man page
end Man page
end<- Man page
extract Man page
extract-methods Man page
getAutomorphisms Man page
getAutomorphisms,AutomorphismList-method Man page
getAutomorphisms,DataFrame_OR_data.frame-method Man page
getAutomorphisms,list-method Man page
getGeneticCode Man page
get_coord Man page
get_coord,BaseGroup_OR_CodonGroup-method Man page
get_coord,DNAStringSet_OR_NULL-method Man page
get_mutscore Man page
get_mutscore,BaseSeq,missing-method Man page
get_mutscore,DNAMultipleAlignment,missing-method Man page
get_mutscore,DNAStringSet,missing-method Man page
get_mutscore,character,character-method Man page
is.url Man page Source code
makeGRangesFromDataFrame Man page
make_zero_col_DataFrame Source code
matrices Man page
matrices,CodonSeq-method Man page
matrices,DNAStringSet_OR_NULL-method Man page
matrices,MatrixList-method Man page
mcols Man page
mcols<- Man page
mod Man page
mod,matrix,numeric-method Man page
modeq Man page Source code
modl Source code
modlin Man page
modlineq Man page
modq Man page
modulo Man page
mut_type Man page Source code
names,AutomorphismList-method Man page
names,ListCodonMatrix-method Man page
names<-,AutomorphismList-method Man page
names<-,MatrixSeq-method Man page
new_SimpleList_from_list Source code
peptide_phychem_index Man page
peptide_phychem_index,DNAStringSet_OR_DNAMultipleAlignment-metho Man page
peptide_phychem_index,character-method Man page
readDNAMultipleAlignment Man page
reexports Man page
rowMeans2 Man page
rowSds Man page
rowSums2 Man page
rowVars Man page
selectAutomorphism Source code
seq2granges Man page
seq2granges,DNAStringSet_OR_NULL-method Man page
seqRanges Man page
seqRanges,CodonSeq-method Man page
seqranges Man page
seqranges,CodonSeq-method Man page
seqranges,DNAStringSet_OR_NULL-method Man page
setValidity2 Man page
show,AutomorphismList-method Man page
show,CodonSeq-method Man page
show,ListCodonMatrix-method Man page
show,MatrixList-method Man page
show,MatrixSeq-method Man page
show-AutomorphismList Man page
show-CodonSeq Man page
show-ListCodonMatrix Man page
show-MatrixList Man page
show-MatrixSeq Man page
slapply Man page Source code
sortByChromAndEnd Man page Source code
sortByChromAndStart Man page Source code
start Man page
start<- Man page
str2chr Man page
str2chr,character-method Man page
str2chr,list-method Man page
str2dig Man page
str2dig,character-method Man page
str2dig,list-method Man page
strand Man page
strand<- Man page
subseq Man page
transl Source code
translate Man page
translation Man page
translation,BioString-method Man page
translation,character-method Man page
unmasked Man page
valid.Automorphism Man page Source code
valid.Automorphism.mcols Man page Source code
valid.AutomorphismByCoef Man page Source code
valid.AutomorphismByCoefList Man page Source code
valid.AutomorphismList Man page Source code
valid.BaseGroup Man page Source code
valid.BaseGroup.elem Man page Source code
valid.CodonGroup Man page Source code
valid.CodonGroup.mcols Man page Source code
valid.ConservedRegion Man page Source code
valid.ConservedRegionList Man page Source code
valid.GRanges Man page Source code
valid.ListCodonMatrix Man page Source code
valid.MatrixList Man page Source code
weighted_manhattan Source code
width Man page
genomaths/GenomAutomorphism documentation built on Jan. 2, 2025, 12:25 a.m.

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