Other packages > Find by keyword >

refdb  

A DNA Reference Library Manager
View on CRAN: Click here


Download and install refdb package within the R console
Install from CRAN:
install.packages("refdb")

Install from Github:
library("remotes")
install_github("cran/refdb")

Install by package version:
library("remotes")
install_version("refdb", "0.1.2")



Attach the package and use:
library("refdb")
Maintained by
Francois Keck
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-09-19
Latest Update:
Description:
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 Bold Systems () and NCBI 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.
How to cite:
Francois Keck (2022). refdb: A DNA Reference Library Manager. R package version 0.1.2, https://cran.r-project.org/web/packages/refdb. Accessed 05 Jun. 2026.
Previous versions and publish date:
0.1.0 (2022-09-19 10:26), 0.1.1 (2022-09-22 19:00), 0.1.2 (2025-12-19 21:20)
Other packages that cited refdb R package
View refdb citation profile
Other R packages that refdb depends, imports, suggests or enhances
Complete documentation for refdb
Functions, R codes and Examples using the refdb R package
Some associated functions: check_fields . fields_dbs . filter_scores . get_ncbi_taxonomy . igraph_from_taxo . make_ncbi_table . ncbi_taxo_rank . process_geo_ncbi . refdb-package . refdb_check_seq_conflict . refdb_check_seq_homogeneity . refdb_check_tax_conflict . refdb_check_tax_typo . refdb_clean_seq_crop_primers . refdb_clean_seq_remove_gaps . refdb_clean_seq_remove_sideN . refdb_clean_tax_NA . refdb_clean_tax_harmonize_nomenclature . refdb_clean_tax_remove_blank . refdb_clean_tax_remove_extra . refdb_clean_tax_remove_subsp . refdb_clean_tax_remove_uncertainty . refdb_export_dada2 . refdb_export_idtaxa . refdb_export_mothur . refdb_fill_tax_downstream . refdb_fill_tax_upstream . refdb_filter_ref_scope . refdb_filter_seq_ambiguous . refdb_filter_seq_duplicates . refdb_filter_seq_homopolymers . refdb_filter_seq_length . refdb_filter_seq_primer . refdb_filter_seq_stopcodon . refdb_filter_tax_na . refdb_filter_tax_precision . refdb_get_fields . refdb_import_BOLD . refdb_import_NCBI . refdb_merge . refdb_plot_map . refdb_plot_seqlen_hist . refdb_plot_tax_barplot . refdb_plot_tax_tree . refdb_plot_tax_treemap . refdb_report . refdb_sample_tax . refdb_set_fields . refdb_set_ncbitax . refdb_write_fields . valid_taxo_rank . xml_extract . 
Some associated R codes: fields.R . import_BOLD.R . import_NCBI.R . refdb-package.R . refdb_checks.R . refdb_clean.R . refdb_export.R . refdb_fill_taxo.R . refdb_filter.R . refdb_merge.R . refdb_ncbi_taxonomy.R . refdb_plots.R . refdb_sample.R .  Full refdb package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

ibb  
R Wrapper for Istanbul Municipality Open Data Portal
Call wrappers for Istanbul Metropolitan Municipality's Open Data Portal (Turkish: Istanbul B ...
Download / Learn more Package Citations See dependency  
envirem  
Generation of ENVIREM Variables
Generation of bioclimatic rasters that are complementary to the typical 19 bioclim variables. ...
Download / Learn more Package Citations See dependency  
quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  
msm  
Multi-State Markov and Hidden Markov Models in Continuous Time
Functions for fitting continuous-time Markov and hidden Markov multi-state models to longitudinal d ...
Download / Learn more Package Citations See dependency  
crossurr  
Cross-Fitting for Doubly Robust Evaluation of High-Dimensional Surrogate Markers
Doubly robust methods for evaluating surrogate markers as outlined in: Agniel D, Hejblum BP, Thiebau ...
Download / Learn more Package Citations See dependency  

27,268

R Packages

233,548

Dependencies

72,590

Author Associations

27,205

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA