Man pages for refdb
A DNA Reference Library Manager

check_fieldsInternal check for fields
fields_dbsFunctions to set fields for various databases
filter_scoresScores for filtering operations
get_ncbi_taxonomyGet NCBI taxonomy
igraph_from_taxoCreate a graph from a taxonomic table
make_ncbi_tableParse NCBI XML and make a table
ncbi_taxo_rankTaxonomic ranks of the NCBI Taxonomy database
process_geo_ncbiProcess coordinate column returned by NCBI
refdb_check_seq_conflictCheck for conflicts in sequences
refdb_check_seq_homogeneityCheck for genetic homogeneity of taxa
refdb_check_tax_conflictCheck for conflicts in taxonomy
refdb_check_tax_typoCheck for typos in taxonomic names
refdb_clean_seq_crop_primersCrop genetic sequences with a set of primers
refdb_clean_seq_remove_gapsRemove gaps from genetic sequences
refdb_clean_seq_remove_sideNRemove repeated side N from genetic sequences
refdb_clean_tax_harmonize_nomenclatureHarmonize taxonomic name nomenclature
refdb_clean_tax_NAConvert missing taxonomic names to NA
refdb_clean_tax_remove_blankRemove blank characters from taxonomic names
refdb_clean_tax_remove_extraRemove extra words from taxonomic names
refdb_clean_tax_remove_subspRemove subspecific information from taxonomic names
refdb_clean_tax_remove_uncertaintyRemove terms indicating uncertainty in taxonomic names
refdb_export_dada2Export reference database for DADA2
refdb_export_idtaxaExport reference database for DECIPHER (IDTAXA)
refdb_export_mothurExport reference database for Mothur
refdb_fill_tax_downstreamFill missing data in taxonomy
refdb_fill_tax_upstreamFill missing data in taxonomy
refdb_filter_ref_scopeFilter records by taxonomic scope of studies
refdb_filter_seq_ambiguousFilter sequences based on their number of ambiguous...
refdb_filter_seq_duplicatesFilter duplicated sequences.
refdb_filter_seq_homopolymersFilter sequences based on their number of repeated character.
refdb_filter_seq_lengthFilter sequences based on their number of character.
refdb_filter_seq_primerFilter sequences based on the presence of primers.
refdb_filter_seq_stopcodonFilter sequences based on their number of of stop codons.
refdb_filter_tax_naFilter records NA taxa
refdb_filter_tax_precisionFilter records based on their taxonomic precision.
refdb_get_fieldsGet fields of a reference database
refdb_import_BOLDDownload and import BOLD records
refdb_import_NCBIDownload and import NCBI Nucleotide records
refdb_mergeMerge reference databases
refdb-packagerefdb: A DNA Reference Library Manager
refdb_plot_mapPlot an interactive map
refdb_plot_seqlen_histPlot an histogram of sequence lengths
refdb_plot_tax_barplotBarplots of the number of records for the most represented...
refdb_plot_tax_treeReference database taxonomy tree
refdb_plot_tax_treemapReference database treemap
refdb_reportCompile a report with different checks
refdb_sample_taxSample records within taxa
refdb_set_fieldsAssociate columns to fields
refdb_set_ncbitaxReplace the current taxonomy using the NCBI Taxonomy database
refdb_write_fieldsWrite fields to a file
valid_taxo_rankRanks considered as valid by refdb
xml_extractExtract XML elements
refdb documentation built on Sept. 22, 2022, 5:07 p.m.