A Toolbox for Manipulating Biological Sequences

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Documentation for package ‘bioseq’ version 0.1.4

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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