A Toolbox for Manipulating Biological Sequences
Remove matched patterns in sequences
Remove a region between two positions in sequences.
Replace a region between two positions in sequences
Reverse translate amino acid sequences
Spell out sequences
Split sequences into k-mers
Split sequences
Compute G+C content
Compute proportions for characters
Translate DNA/RNA sequences into amino acids
Transcribe DNA, reverse-transcribe RNA
Sequence validator
Write sequences in FASTA format
Build an amino acid (AA) vector
AliView: DNA sequences viewer
Biological alphabets
Convert DNAbin/AAbin to tibble
Convert bioseq DNA, RNA and AA to tibble
Coercion to an amino acid (AA) vector
Coerce to AAbin
Coerce tibble to AAbin
Coercion to DNA vector
Coerce to DNAbin
Coerce tibble to DNAbin
Coercion to RNA vector
Coerce to seqinr alignment
bioseq: A Toolbox for Manipulating Biological Sequences
Genetic code tables
Build a DNA vector
Genetic code tables
Internal
Test if the object is an amino acid vector
Test if the object is a DNA vector
Test if the object is a RNA vector
Amino acid (AA) vector constructor
DNA vector constructor
RNA vector constructor
Internal formatting
Internal formatting
Internal formatting
Read sequences in FASTA format
Reverse and complement sequences
Build a RNA vector
SeaView: DNA sequences and phylogenetic tree viewer
Replace matched patterns in sequences
Cluster sequences by similarity
Combine multiple sequences
Find a consensus sequence for a set of sequences.
Count the number of matches in sequences
Crop sequences using delimiting patterns
Crop sequences between two positions
Detect the presence of patterns in sequences
Disambiguate biological sequences
Extract matching patterns from sequences
Extract a region between two positions in sequences
Count the number of character in sequences
Number of sequences in a vector
Classes and functions to work with biological sequences (DNA, RNA and amino acid sequences). Implements S3 infrastructure to work with biological sequences as described in Keck (2020) <doi:10.1111/2041-210X.13490>. Provides a collection of functions to perform biological conversion among classes (transcription, translation) and basic operations on sequences (detection, selection and replacement based on positions or patterns). The package also provides functions to import and export sequences from and to other package formats.