Package: refdb 0.1.3

refdb: A DNA Reference Library Manager

Reference database manager offering a set of functions to import, organize, clean, filter, audit and export reference genetic data. Provide functions to download sequence data from NCBI GenBank <https://www.ncbi.nlm.nih.gov/genbank/>. Designed as an environment for semi-automatic and assisted construction of reference databases and to improve standardization and repeatability in barcoding and metabarcoding studies.

Authors:Francois Keck [aut, cre, cph]

refdb_0.1.3.tar.gz
refdb_0.1.3.zip(r-4.7)refdb_0.1.3.zip(r-4.6)refdb_0.1.3.zip(r-4.5)
refdb_0.1.3.tgz(r-4.6-any)refdb_0.1.3.tgz(r-4.5-any)
refdb_0.1.3.tar.gz(r-4.7-any)refdb_0.1.3.tar.gz(r-4.6-any)
refdb_0.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
refdb/json (API)

# Install 'refdb' in R:
install.packages('refdb', repos = c('https://fkeck.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fkeck/refdb/issues

Pkgdown/docs site:https://fkeck.github.io

On CRAN:

Conda:

5.80 score 13 stars 12 scripts 207 downloads 45 exports 127 dependencies

Last updated from:40eca7c957. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK171
source / vignettesOK222
linux-release-x86_64OK174
macos-release-arm64OK130
macos-oldrel-arm64OK94
windows-develOK152
windows-releaseOK103
windows-oldrelOK98
wasm-releaseOK149

Exports:refdb_check_seq_conflictrefdb_check_seq_homogeneityrefdb_check_tax_conflictrefdb_check_tax_typorefdb_clean_seq_crop_primersrefdb_clean_seq_remove_gapsrefdb_clean_seq_remove_sideNrefdb_clean_tax_harmonize_nomenclaturerefdb_clean_tax_NArefdb_clean_tax_remove_blankrefdb_clean_tax_remove_extrarefdb_clean_tax_remove_subsprefdb_clean_tax_remove_uncertaintyrefdb_export_dada2refdb_export_idtaxarefdb_export_mothurrefdb_export_utaxrefdb_fill_tax_downstreamrefdb_fill_tax_upstreamrefdb_filter_ref_scoperefdb_filter_seq_ambiguousrefdb_filter_seq_duplicatesrefdb_filter_seq_homopolymersrefdb_filter_seq_lengthrefdb_filter_seq_primerrefdb_filter_seq_stopcodonrefdb_filter_tax_narefdb_filter_tax_precisionrefdb_get_fieldsrefdb_import_NCBIrefdb_mergerefdb_plot_maprefdb_plot_seqlen_histrefdb_plot_tax_barplotrefdb_plot_tax_treerefdb_plot_tax_treemaprefdb_reportrefdb_set_fieldsrefdb_set_fields_BOLDrefdb_set_fields_diatbarcoderefdb_set_fields_NCBIrefdb_set_fields_PR2refdb_set_ncbitaxrefdb_write_fieldsvalid_taxo_rank

Dependencies:apeaskpassbase64encbioseqbitbit64bslibcachemclassclassIntclicliprcpp11crayoncrosstalkcrulcurldata.tableDBIdigestdplyre1071evaluatefarverfastmapfastmatchfontawesomefsgenericsggforceggplot2ggraphggrepelgluegraphlayoutsgridExtragtablehighrhmshtmltoolshtmlwidgetshttpcodehttrigraphisobandjquerylibjsonliteKernSmoothknitrlabelinglatticelazyevalleafletleaflet.providerslifecyclemagrittrMASSMatrixmemoisemimenatservnlmeopensslphangornpillarpkgconfigplyrpngpolyclipprettyunitsprogressproxypurrrquadprogR6rappdirsrasterRColorBrewerRcppRcppArmadilloreadrrentrezritisrlangrmarkdownrnclrotlrredlists2S7sassscalessfsolriumspstringdiststringistringrsyssystemfontstaxizeterratibbletidygraphtidyrtidyselecttinytextriebeardtweenrtzdbunitsurltoolsutf8vctrsviridisviridisLitevroomWikipediRwikitaxawithrwkworrmsxfunXMLxml2yamlzoo

Downloading and combining data from NCBI Genbank and BOLD

Rendered fromncbi_bold.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2021-11-11
Started: 2021-10-07

Introduction to the refdb package

Rendered fromintro_refdb.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2021-11-11
Started: 2021-09-03

Readme and manuals

Help Manual

Help pageTopics
Internal check for fieldscheck_fields
Functions to set fields for various databasesfields_dbs refdb_set_fields_BOLD refdb_set_fields_diatbarcode refdb_set_fields_NCBI refdb_set_fields_PR2
Scores for filtering operations.filter_seq_length filter_scores
Get NCBI taxonomyget_ncbi_taxonomy
Create a graph from a taxonomic tableigraph_from_taxo
Parse NCBI XML and make a tablemake_ncbi_table
Taxonomic ranks of the NCBI Taxonomy databasencbi_taxo_rank
Process coordinate column returned by NCBIprocess_geo_ncbi
Check for conflicts in sequencesrefdb_check_seq_conflict
Check for genetic homogeneity of taxarefdb_check_seq_homogeneity
Check for conflicts in taxonomyrefdb_check_tax_conflict
Check for typos in taxonomic namesrefdb_check_tax_typo
Crop genetic sequences with a set of primersrefdb_clean_seq_crop_primers
Remove gaps from genetic sequencesrefdb_clean_seq_remove_gaps
Remove repeated side N from genetic sequencesrefdb_clean_seq_remove_sideN
Harmonize taxonomic name nomenclaturerefdb_clean_tax_harmonize_nomenclature
Convert missing taxonomic names to NArefdb_clean_tax_NA
Remove blank characters from taxonomic namesrefdb_clean_tax_remove_blank
Remove extra words from taxonomic namesrefdb_clean_tax_remove_extra
Remove subspecific information from taxonomic namesrefdb_clean_tax_remove_subsp
Remove terms indicating uncertainty in taxonomic namesrefdb_clean_tax_remove_uncertainty
Export reference database for DADA2refdb_export_dada2
Export reference database for DECIPHER (IDTAXA)refdb_export_idtaxa
Export reference database for Mothurrefdb_export_mothur
Export reference database for USEARCH/VSEARCHrefdb_export_utax
Fill missing data in taxonomyrefdb_fill_tax_downstream
Fill missing data in taxonomyrefdb_fill_tax_upstream
Filter records by taxonomic scope of studiesrefdb_filter_ref_scope
Filter sequences based on their number of ambiguous character.refdb_filter_seq_ambiguous
Filter duplicated sequences.refdb_filter_seq_duplicates
Filter sequences based on their number of repeated character.refdb_filter_seq_homopolymers
Filter sequences based on their number of character.refdb_filter_seq_length
Filter sequences based on the presence of primers.refdb_filter_seq_primer
Filter sequences based on their number of of stop codons.refdb_filter_seq_stopcodon
Filter records NA taxarefdb_filter_tax_na
Filter records based on their taxonomic precision.refdb_filter_tax_precision
Get fields of a reference databaserefdb_get_fields
Download and import NCBI Nucleotide recordsrefdb_import_NCBI
Merge reference databasesrefdb_merge
Plot an interactive maprefdb_plot_map
Plot an histogram of sequence lengthsrefdb_plot_seqlen_hist
Barplots of the number of records for the most represented taxarefdb_plot_tax_barplot
Reference database taxonomy treerefdb_plot_tax_tree
Reference database treemaprefdb_plot_tax_treemap
Compile a report with different checksrefdb_report
Sample records within taxarefdb_sample_tax
Associate columns to fieldsrefdb_set_fields
Replace the current taxonomy using the NCBI Taxonomy databaserefdb_set_ncbitax
Write fields to a filerefdb_write_fields
Ranks considered as valid by refdbvalid_taxo_rank
Extract XML elementsxml_extract