Man pages for refdb
A DNA Reference Library Manager
| 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... |
| 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-package | refdb: A DNA Reference Library Manager |
| 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... |
| 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 |
