refdb0.1.2 package

Internal check for fields

Functions to set fields for various databases

Scores for filtering operations

Get NCBI taxonomy

Create a graph from a taxonomic table

Parse NCBI XML and make a table

Taxonomic ranks of the NCBI Taxonomy database

Process coordinate column returned by NCBI

refdb: A DNA Reference Library Manager

Check for conflicts in sequences

Check for genetic homogeneity of taxa

Check for conflicts in taxonomy

Check for typos in taxonomic names

Crop genetic sequences with a set of primers

Remove gaps from genetic sequences

Remove repeated side N from genetic sequences

Harmonize taxonomic name nomenclature

Convert missing taxonomic names to NA

Remove blank characters from taxonomic names

Remove extra words from taxonomic names

Remove subspecific information from taxonomic names

Remove terms indicating uncertainty in taxonomic names

Export reference database for DADA2

Export reference database for DECIPHER (IDTAXA)

Export reference database for Mothur

Fill missing data in taxonomy

Fill missing data in taxonomy

Filter records by taxonomic scope of studies

Filter sequences based on their number of ambiguous character.

Filter duplicated sequences.

Filter sequences based on their number of repeated character.

Filter sequences based on their number of character.

Filter sequences based on the presence of primers.

Filter sequences based on their number of of stop codons.

Filter records NA taxa

Filter records based on their taxonomic precision.

Get fields of a reference database

Download and import BOLD records

Download and import NCBI Nucleotide records

Merge reference databases

Plot an interactive map

Plot an histogram of sequence lengths

Barplots of the number of records for the most represented taxa

Reference database taxonomy tree

Reference database treemap

Compile a report with different checks

Sample records within taxa

Associate columns to fields

Replace the current taxonomy using the NCBI Taxonomy database

Write fields to a file

Ranks considered as valid by refdb

Extract XML elements