Files in alexpiper/taxreturn

An R package for retrieving and curating public DNA barcode reference data

LICENSE.md NEWS.md R/DNAbin_utilities.R R/blast_utilities.R R/data.R R/deprecated.R R/fetch_sequences.R R/filter_sequences.R R/helper_functions.R R/ncbi_taxonomy.R R/ott_taxonomy.R R/tax_utilities.R R/utilities.R README.Rmd README.md data-raw/DATASET.R doc/taxreturn-vignette.R doc/taxreturn-vignette.Rmd man/DNAbin2DNAstringset.Rd man/DNAbin2char.Rd man/acc2hex.Rd man/acc_from_fasta.Rd man/alignment_entropy.Rd man/blast.Rd man/blast_assign_species.Rd man/blast_install.Rd man/blast_params.Rd man/blast_top_hit.Rd man/char2DNAbin.Rd man/clean_seqs.Rd man/closest_seq.Rd man/codon_entropy.Rd man/codon_filter.Rd man/concat_DNAbin.Rd man/dot-findExecutable.Rd man/dot-hex.Rd man/dot-ishex.Rd man/dot-unhex.Rd man/download_ott_taxonomy.Rd man/fetchSeqs.Rd man/fetch_bold.Rd man/fetch_genbank.Rd man/fetch_seqs.Rd man/filter_by_tax.Rd man/filter_infraspecifc.Rd man/filter_unplaced.Rd man/get_binding_position.Rd man/get_mixed_clusters.Rd man/get_ncbi_lineage.Rd man/get_ncbi_synonyms.Rd man/get_ncbi_taxonomy.Rd man/get_ott_lineage.Rd man/get_ott_taxonomy.Rd man/get_reading_frame.Rd man/get_subalignment.Rd man/gid_to_acc.Rd man/graft_tips.Rd man/hex2acc.Rd man/kmer_screen.Rd man/lca_probs.Rd man/make_blast_db.Rd man/makeblastdb.Rd man/map_to_model.Rd man/map_to_ott.Rd man/model.Rd man/ncbi_taxid.Rd man/pad_alignment.Rd man/parse_gb.Rd man/parse_ott_synonyms.Rd man/pipe.Rd man/propagate_tax.Rd man/prune_groups.Rd man/random_seq.Rd man/read_bold_chunk.Rd man/read_genbank_chunk.Rd man/reformat_dada2_gen.Rd man/reformat_dada2_spp.Rd man/reformat_hierarchy.Rd man/resolve_synonyms_ncbi.Rd man/setup_multithread.Rd man/setup_para.Rd man/split_bold_query.Rd man/subset_model.Rd man/summarise_fasta.Rd man/tax2phylo.Rd man/tax2tree.Rd man/train_idtaxa.Rd man/write_fasta.Rd tests/spelling.R tests/testthat.R tests/testthat/test-data.R vignettes/taxreturn.Rmd