Tidy Processing and Analysis of Biological Sequences
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Documentation for package ‘tidysq’ version 1.1.3
Help Pages
| 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 |