Package index • barcodeMineR

Taxonomy

Search taxa on DNA repository

get_bold_taxonomy(): Get taxonomic classification of the BOLD taxonomy database for a list of taxa

get_ncbi_taxonomy(): Get taxonomic classification of the NCBI taxonomy database for a list of taxa or taxids

Download

Download records from DNA repository

download_bold(): Download records from BOLD

download_ncbi(): Download records from the NCBI

Others

Additional functions

mergeBarcodeOres(): Merge multiple refdb objects to create a single one

loadBarcodeOre(): Load sequences and corresponding records as a refdb object

Plots

Functions using ggplot2 and ggridges to visualize a barcodeOre

plot_length(): Show the length reduction for the downloaded sequences as a Bar plot

plot_primers(): Show the primers' names as a Bubble plot

Example Datasets

Example datasets used to describe the required formats

example_record: Example records data frame

example_sequence: Example DNAStringSet sequence

species200: Example dataset of 200 species names