check_fields            Internal check for fields
fields_dbs              Functions to set fields for various databases
filter_scores           Scores for filtering operations
get_ncbi_taxonomy       Get NCBI taxonomy
igraph_from_taxo        Create a graph from a taxonomic table
make_ncbi_table         Parse NCBI XML and make a table
ncbi_taxo_rank          Taxonomic ranks of the NCBI Taxonomy database
process_geo_ncbi        Process coordinate column returned by NCBI
refdb_check_seq_conflict
                        Check for conflicts in sequences
refdb_check_seq_homogeneity
                        Check for genetic homogeneity of taxa
refdb_check_tax_conflict
                        Check for conflicts in taxonomy
refdb_check_tax_typo    Check for typos in taxonomic names
refdb_clean_seq_crop_primers
                        Crop genetic sequences with a set of primers
refdb_clean_seq_remove_gaps
                        Remove gaps from genetic sequences
refdb_clean_seq_remove_sideN
                        Remove repeated side N from genetic sequences
refdb_clean_tax_NA      Convert missing taxonomic names to NA
refdb_clean_tax_harmonize_nomenclature
                        Harmonize taxonomic name nomenclature
refdb_clean_tax_remove_blank
                        Remove blank characters from taxonomic names
refdb_clean_tax_remove_extra
                        Remove extra words from taxonomic names
refdb_clean_tax_remove_subsp
                        Remove subspecific information from taxonomic
                        names
refdb_clean_tax_remove_uncertainty
                        Remove terms indicating uncertainty in
                        taxonomic names
refdb_export_dada2      Export reference database for DADA2
refdb_export_idtaxa     Export reference database for DECIPHER (IDTAXA)
refdb_export_mothur     Export reference database for Mothur
refdb_export_utax       Export reference database for USEARCH/VSEARCH
refdb_fill_tax_downstream
                        Fill missing data in taxonomy
refdb_fill_tax_upstream
                        Fill missing data in taxonomy
refdb_filter_ref_scope
                        Filter records by taxonomic scope of studies
refdb_filter_seq_ambiguous
                        Filter sequences based on their number of
                        ambiguous character.
refdb_filter_seq_duplicates
                        Filter duplicated sequences.
refdb_filter_seq_homopolymers
                        Filter sequences based on their number of
                        repeated character.
refdb_filter_seq_length
                        Filter sequences based on their number of
                        character.
refdb_filter_seq_primer
                        Filter sequences based on the presence of
                        primers.
refdb_filter_seq_stopcodon
                        Filter sequences based on their number of of
                        stop codons.
refdb_filter_tax_na     Filter records NA taxa
refdb_filter_tax_precision
                        Filter records based on their taxonomic
                        precision.
refdb_get_fields        Get fields of a reference database
refdb_import_NCBI       Download and import NCBI Nucleotide records
refdb_merge             Merge reference databases
refdb_plot_map          Plot an interactive map
refdb_plot_seqlen_hist
                        Plot an histogram of sequence lengths
refdb_plot_tax_barplot
                        Barplots of the number of records for the most
                        represented taxa
refdb_plot_tax_tree     Reference database taxonomy tree
refdb_plot_tax_treemap
                        Reference database treemap
refdb_report            Compile a report with different checks
refdb_sample_tax        Sample records within taxa
refdb_set_fields        Associate columns to fields
refdb_set_ncbitax       Replace the current taxonomy using the NCBI
                        Taxonomy database
refdb_write_fields      Write fields to a file
valid_taxo_rank         Ranks considered as valid by refdb
xml_extract             Extract XML elements
