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bioseq: A Toolbox for Manipulating Biological Sequences in R

The purpose of bioseq is to provide a collection of classes and functions for biological sequence manipulation in R. The package provides simple S3 classes for sequences that are suitable for inclusion in a data frame and that can be analysed using the dplyr grammar and other tidyverse tools.

Installation

You can install the development version of bioseq from GitHub with:

remotes::install_github("fkeck/bioseq")

Tutorials

There are two vignettes available to get started with the package:

  • Introduction to the bioseq package
  • Cleaning and exploring NCBI data with the bioseq package

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Version

Install

install.packages('bioseq')

Monthly Downloads

505

Version

0.1.1

License

GPL-3

Maintainer

Francois Keck

Last Published

July 26th, 2020

Functions in bioseq (0.1.1)

alphabets

Biological alphabets
aliview

AliView: DNA sequences viewer
as_aa

Coercion to an amino acid (AA) vector
as_DNAbin.tbl_df

Coerce tibble to DNAbin
as_DNAbin

Coerce to DNAbin
aa

Build an amino acid (AA) vector
as-tibble-ape

Convert DNAbin/AAbin to tibble
as-tibble-bioseq

Convert bioseq DNA, RNA and AA to tibble
as_AAbin.tbl_df

Coerce tibble to AAbin
as_AAbin

Coerce to AAbin
fragilaria

DNA sequences (rbcL) for various Fragilaria
new_aa

Amino acid (AA) vector constructor
new_dna

DNA vector constructor
genetic-codes

Genetic code tables
pillar_shaft.bioseq_rna

Internal formatting
seq_replace_position

Replace a region between two positions in sequences
seq_detect_pattern

Detect the presence of patterns in sequences
seq_crop_position

Crop sequences between two positions
seq_remove_position

Remove a region between two positions in sequences.
as_seqinr_alignment

Coerce to seqinr alignment
seq_rev_translate

Reverse translate amino acid sequences
pillar_shaft.bioseq_dna

Internal formatting
bioseq-package

bioseq: A Toolbox for Manipulating Biological Sequences
seq_split_kmer

Split sequences into k-mers
vec_ptype2.bioseq_aa

Internal
as_rna

Coercion to RNA vector
as_dna

Coercion to DNA vector
seq_spellout

Spell out sequences
validate_seq

Sequence validator
write_fasta

Write sequences in FASTA format
seq_split_pattern

Split sequences
is_rna

Test if the object is a RNA vector
dna

Build a DNA vector
seq_cluster

Cluster sequences by similarity
dic_genetic_codes

Genetic code tables
is_dna

Test if the object is a DNA vector
seq-replace

Replace matched patterns in sequences
rna

Build a RNA vector
is_aa

Test if the object is an amino acid vector
read_fasta

Read sequences in FASTA format
new_rna

RNA vector constructor
seq_stat_gc

Compute G+C content
seq_stat_prop

Compute proportions for characters
seq_translate

Translate DNA/RNA sequences into amino acids
seq_nseq

Number of sequences in a vector
seq_combine

Combine multiple sequences
rev_complement

Reverse and complement sequences
seq_consensus

Find a consensus sequence for a set of sequences.
seq_remove_pattern

Remove matched patterns in sequences
pillar_shaft.bioseq_aa

Internal formatting
seq_count_pattern

Count the number of matches in sequences
seaview

SeaView: DNA sequences and phylogenetic tree viewer
transcription

Transcribe DNA, reverse-transcribe RNA
seq_crop_pattern

Crop sequences using delimiting patterns
seq_nchar

Count the number of character in sequences
seq_extract_position

Extract a region between two positions in sequences
seq_disambiguate_IUPAC

Disambiguate biological sequences
seq_extract_pattern

Extract matching patterns from sequences