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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", "0.1.1")



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: 2022-09-22
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 (<https://www.boldsystems.org/>) and 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.
How to cite:
Francois Keck (2022). refdb: A DNA Reference Library Manager. R package version 0.1.1, https://cran.r-project.org/web/packages/refdb
Previous versions and publish date:
0.1.0 (2022-09-19 10:26)
Other packages that cited refdb R package
View refdb citation profile
Other R packages that refdb depends, imports, suggests or enhances
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
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