A Toolbox for Manipulating Biological Sequences
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Documentation for package ‘bioseq’ version 0.1.4
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 |