R: A DNA Reference Library Manager

# A DNA Reference Library Manager

## Documentation for package ‘refdb’ version 0.1.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

.filter_seq_length | Scores for filtering operations
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_harmonize_nomenclature | Harmonize taxonomic name nomenclature
refdb_clean_tax_NA | Convert missing taxonomic names to NA
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_fields_BOLD | Functions to set fields for various databases
refdb_set_fields_diatbarcode | Functions to set fields for various databases
refdb_set_fields_NCBI | Functions to set fields for various databases
refdb_set_fields_PR2 | Functions to set fields for various databases
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