Package: refdb 0.1.1

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 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.

Authors:Francois Keck [aut, cre, cph]

refdb_0.1.1.tar.gz
refdb_0.1.1.zip(r-4.5)refdb_0.1.1.zip(r-4.4)refdb_0.1.1.zip(r-4.3)
refdb_0.1.1.tgz(r-4.4-any)refdb_0.1.1.tgz(r-4.3-any)
refdb_0.1.1.tar.gz(r-4.5-noble)refdb_0.1.1.tar.gz(r-4.4-noble)
refdb_0.1.1.tgz(r-4.4-emscripten)refdb_0.1.1.tgz(r-4.3-emscripten)
refdb.pdf |refdb.html✨
refdb/json (API)

Peer review:

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

On CRAN:

46 exports 11 stars 1.52 score 143 dependencies 9 scripts 165 downloads

Last updated 1 years agofrom:2c2750475f. Checks:OK: 3 NOTE: 4. Indexed: yes.

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_BOLDrefdb_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:apeaskpassassertthatbackportsbase64encbioseqbitbit64boldbslibcachemcheckmateclicliprclustercodetoolscolorspaceconditionzcpp11crayoncrosstalkcrulcurldata.tabledigestdplyrevaluatefansifarverfastmapfastmatchfontawesomeforeachforeignFormulafsgenericsggforceggplot2ggraphggrepelgluegraphlayoutsgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpcodehttrigraphisobanditeratorsjquerylibjsonliteknitrlabelinglatticelazyevalleafletleaflet.providerslifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnatservnlmennetopensslpbapplyphangornpillarpkgconfigplyrpngpolyclipprettyunitsprogresspurrrquadprogR6rappdirsrasterratelimitrRColorBrewerRcppRcppArmadilloRcppEigenreadrrentrezrexritisrlangrmarkdownrnclrotlrpartrredlistrstudioapisassscalessolriumspstringdiststringistringrsyssystemfontstaxizeterratibbletidygraphtidyrtidyselecttinytextriebeardtweenrtzdburltoolsutf8uuidvctrsviridisviridisLitevroomWikidataQueryServiceRWikidataRWikipediRwikitaxawithrworrmsxfunXMLxml2yamlzoo