.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_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_BOLD |
Download and import BOLD records |
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 |