R: A Toolbox for Manipulating Biological Sequences

# A Toolbox for Manipulating Biological Sequences

## Documentation for package ‘bioseq’ version 0.1.5

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

aa | Build an amino acid (AA) vector
aliview | AliView: DNA sequences viewer
alphabets | Biological alphabets
as-tibble-ape | Convert DNAbin/AAbin to tibble
as-tibble-bioseq | Convert bioseq DNA, RNA and AA to tibble
as_aa | Coercion to an amino acid (AA) vector
as_AAbin | Coerce to AAbin
as_AAbin.tbl_df | Coerce tibble to AAbin
as_dna | Coercion to DNA vector
as_DNAbin | Coerce to DNAbin
as_DNAbin.tbl_df | Coerce tibble to DNAbin
as_rna | Coercion to RNA vector
as_seqinr_alignment | Coerce to seqinr alignment
as_tibble.AAbin | Convert DNAbin/AAbin to tibble
as_tibble.bioseq_aa | Convert bioseq DNA, RNA and AA to tibble
as_tibble.bioseq_dna | Convert bioseq DNA, RNA and AA to tibble
as_tibble.bioseq_rna | Convert bioseq DNA, RNA and AA to tibble
as_tibble.DNAbin | Convert DNAbin/AAbin to tibble
dic_genetic_codes | Genetic code tables
dna | Build a DNA vector
fragilaria | DNA sequences (rbcL) for various Fragilaria
genetic-codes | Genetic code tables
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
new_aa | Amino acid (AA) vector constructor
new_dna | DNA vector constructor
new_rna | RNA vector constructor
read_fasta | Read sequences in FASTA format
rev_complement | Reverse and complement sequences
rna | Build a RNA vector
seaview | SeaView: DNA sequences and phylogenetic tree viewer
seq-replace | Replace matched patterns in sequences
seq_cluster | Cluster sequences by similarity
seq_combine | Combine multiple sequences
seq_complement | Reverse and complement sequences
seq_consensus | Find a consensus sequence for a set of 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_disambiguate_IUPAC | Disambiguate biological sequences
seq_extract_pattern | Extract matching patterns from sequences
seq_extract_position | Extract a region between two positions in sequences
seq_nchar | Count the number of character in sequences
seq_nseq | Number of sequences in a vector
seq_remove_pattern | Remove matched patterns in sequences
seq_remove_position | Remove a region between two positions in sequences.
seq_replace_pattern | Replace matched patterns in sequences
seq_replace_position | Replace a region between two positions in sequences
seq_reverse | Reverse and complement sequences
seq_rev_transcribe | Transcribe DNA, reverse-transcribe RNA
seq_rev_translate | Reverse translate amino acid sequences
seq_spellout | Spell out sequences
seq_split_kmer | Split sequences into k-mers
seq_split_pattern | Split sequences
seq_stat_gc | Compute G+C content
seq_stat_prop | Compute proportions for characters
seq_transcribe | Transcribe DNA, reverse-transcribe RNA
seq_translate | Translate DNA/RNA sequences into amino acids
transcription | Transcribe DNA, reverse-transcribe RNA
write_fasta | Write sequences in FASTA format