tidysq-package |
tidysq: tidy analysis of biological sequences |
%has% |
Test sq object for presence of given motifs |
==.sq |
Compare sq objects |
alphabet |
Get alphabet of given sq object. |
as.character.sq |
Convert sq object into character vector |
as.matrix.sq |
Convert sq object into matrix |
as.sq |
Convert an object to sq |
as.sq.character |
Convert an object to sq |
as.sq.default |
Convert an object to sq |
bite |
Subset sequences from sq objects |
bite.sq |
Subset sequences from sq objects |
collapse |
Collapse multiple sequences into one |
collapse.sq |
Collapse multiple sequences into one |
complement |
Create complement sequence from dnasq or rnasq object |
complement.sq_dna_bsc |
Create complement sequence from dnasq or rnasq object |
complement.sq_dna_ext |
Create complement sequence from dnasq or rnasq object |
complement.sq_rna_bsc |
Create complement sequence from dnasq or rnasq object |
complement.sq_rna_ext |
Create complement sequence from dnasq or rnasq object |
export_sq |
Export sq objects into other formats |
find_invalid_letters |
Find elements which are not suitable for specified type. |
find_invalid_letters.sq |
Find elements which are not suitable for specified type. |
find_motifs |
Find given motifs |
find_motifs.sq |
Find given motifs |
get_sq_lengths |
Get lengths of sequences in sq object |
get_standard_alphabet |
Get standard alphabet for given type. |
get_tidysq_options |
Obtain current state of tidysq options |
import_sq |
Import sq objects from other objects |
is.sq |
Check if object has specified type |
is.sq_ami |
Check if object has specified type |
is.sq_ami_bsc |
Check if object has specified type |
is.sq_ami_ext |
Check if object has specified type |
is.sq_atp |
Check if object has specified type |
is.sq_dna |
Check if object has specified type |
is.sq_dna_bsc |
Check if object has specified type |
is.sq_dna_ext |
Check if object has specified type |
is.sq_rna |
Check if object has specified type |
is.sq_rna_bsc |
Check if object has specified type |
is.sq_rna_ext |
Check if object has specified type |
is.sq_unt |
Check if object has specified type |
is_empty_sq |
Test if sequence is empty |
paste |
Paste sequences in string-like fashion |
paste.sq |
Paste sequences in string-like fashion |
random_sq |
Generate random sequences |
read_fasta |
Read a FASTA file |
remove_ambiguous |
Remove sequences that contain ambiguous elements |
remove_ambiguous.sq |
Remove sequences that contain ambiguous elements |
remove_na |
Remove sequences that contain NA values |
remove_na.sq |
Remove sequences that contain NA values |
reverse |
Reverse sequence |
reverse.sq |
Reverse sequence |
sq |
Construct sq object from character vector |
sq-class |
sq: class for keeping biological sequences tidy |
sq-concatenate |
Concatenate sq objects |
sq-extract |
Extract parts of a sq object |
sq-print |
Print sq object |
sqapply |
Apply function to each sequence |
sqconcatenate |
Concatenate sq objects |
sqextract |
Extract parts of a sq object |
sqprint |
Print sq object |
sq_type |
Get type of an sq object |
sq_type.sq |
Get type of an sq object |
sq_type<- |
Get type of an sq object |
sq_type<-.sq |
Get type of an sq object |
substitute_letters |
Substitute letters in a sequence |
substitute_letters.sq |
Substitute letters in a sequence |
tidysq |
tidysq: tidy analysis of biological sequences |
tidysq-options |
Obtain current state of tidysq options |
translate |
Convert DNA or RNA into proteins using genetic code |
translate.sq_dna_bsc |
Convert DNA or RNA into proteins using genetic code |
translate.sq_rna_bsc |
Convert DNA or RNA into proteins using genetic code |
typify |
Set type of an sq object |
typify.sq |
Set type of an sq object |
write_fasta |
Save sq to fasta file |