Function reference • bioseq

Biological sequence classes
`aa()`	Build an amino acid (AA) vector
`dna()`	Build a DNA vector
`rna()`	Build a RNA vector
`new_aa()`	Amino acid (AA) vector constructor
`new_dna()`	DNA vector constructor
`new_rna()`	RNA vector constructor
`is_aa()`	Test if the object is an amino acid vector
`is_dna()`	Test if the object is a DNA vector
`is_rna()`	Test if the object is a RNA vector
Conversion and coercion
`as_tibble.DNAbin()` `as_tibble.AAbin()`	Convert DNAbin/AAbin to tibble
`as_tibble.bioseq_dna()` `as_tibble.bioseq_rna()` `as_tibble.bioseq_aa()`	Convert bioseq DNA, RNA and AA to tibble
`as_AAbin()`	Coerce to AAbin
`as_AAbin(<tbl_df>)`	Coerce tibble to AAbin
`as_DNAbin()`	Coerce to DNAbin
`as_DNAbin(<tbl_df>)`	Coerce tibble to DNAbin
`as_aa()`	Coercion to an amino acid (AA) vector
`as_dna()`	Coercion to DNA vector
`as_rna()`	Coercion to RNA vector
`as_seqinr_alignment()`	Coerce to seqinr alignment
Data
`fragilaria`	DNA sequences (rbcL) for various Fragilaria
I/O
`read_fasta()`	Read sequences in FASTA format
`write_fasta()`	Write sequences in FASTA format
GUI
`aliview()`	AliView: DNA sequences viewer
`seaview()`	SeaView: DNA sequences and phylogenetic tree viewer
Operations on sequences
Biological operations
`seq_complement()` `seq_reverse()`	Reverse and complement sequences
`seq_rev_translate()`	Reverse translate amino acid sequences
`seq_translate()`	Translate DNA/RNA sequences into amino acids
`seq_transcribe()` `seq_rev_transcribe()`	Transcribe DNA, reverse-transcribe RNA
String-related operations
`seq_replace_pattern()`	Replace matched patterns in sequences
`seq_combine()`	Combine multiple sequences
`seq_count_pattern()`	Count the number of matches in sequences
`seq_crop_pattern()`	Crop sequences using delimiting patterns
`seq_crop_position()`	Crop sequences between two positions
`seq_detect_pattern()`	Detect the presence of patterns in sequences
`seq_extract_pattern()`	Extract matching patterns from sequences
`seq_extract_position()`	Extract a region between two positions in sequences
`seq_remove_pattern()`	Remove matched patterns in sequences
`seq_remove_position()`	Remove a region between two positions in sequences.
`seq_replace_position()`	Replace a region between two positions in sequences
`seq_split_kmer()`	Split sequences into k-mers
`seq_split_pattern()`	Split sequences
Aggregate operations
`seq_cluster()`	Cluster sequences by similarity
`seq_consensus()`	Find a consensus sequence for a set of sequences.
Utilities
`seq_nseq()`	Number of sequences in a vector
`seq_nchar()`	Count the number of character in sequences
`seq_stat_prop()`	Compute proportions for characters
`seq_stat_gc()`	Compute G+C content
`seq_disambiguate_IUPAC()`	Disambiguate biological sequences
`seq_spellout()`	Spell out sequences
Genetic codes and alphabets
`alphabets`	Biological alphabets
`dic_genetic_codes()`	Genetic code tables
`genetic-codes`	Genetic code tables

Reference

Biological sequence classes

Conversion and coercion

Data

I/O

GUI

Operations on sequences

Biological operations

String-related operations

Aggregate operations

Utilities

Genetic codes and alphabets