Man pages for alexpiper/taxreturn
An R package for retrieving and curating public DNA barcode reference data
| acc2hex | Convert accession number to hexadecimal coding |
| acc_from_fasta | Genbank accessions from fasta |
| alignment_entropy | Alignment entropy |
| blast | Run BLAST search |
| blast_assign_species | Assign species using BLAST |
| blast_install | Install BLAST |
| blast_params | Show BLAST parameters |
| blast_top_hit | BLAST Top Hit |
| char2DNAbin | char2DNAbin |
| clean_seqs | Clean Sequences with PHMM (DEPRECATED) |
| closest_seq | Closest kmer distance This function checks the kmer distance... |
| codon_entropy | Codon entropy |
| codon_filter | Filter sequences containing stop codons |
| concat_DNAbin | Concatenate DNAbin objects while preserving attributes. This... |
| DNAbin2char | DNAbin to char |
| DNAbin2DNAstringset | Convert DNABin to DNAStringSet |
| dot-findExecutable | Find executable |
| dot-hex | convert alphanumerics to hexadecimal internal taxreturn... |
| dot-ishex | Check whether a string is hexadecimal internal taxreturn... |
| dot-unhex | convert hexadecimal strings to alphanumeric internal... |
| download_ott_taxonomy | Download open tree of life taxonomy |
| fetch_bold | Fetch sequences from BOLD |
| fetch_genbank | all [filter] Retrieves everthing Specified [property] Formal... |
| fetch_seqs | fetch_seqs function |
| fetchSeqs | Fetchseqs function (DEPRECATED) |
| filter_by_tax | Filter sequences by taxonomy |
| filter_infraspecifc | Filter infraspecific taxonomic labels |
| filter_unplaced | Filter unplaced taxonomic labels |
| get_binding_position | Get primer binding position |
| get_mixed_clusters | Get mixed clusters |
| get_ncbi_lineage | Get lineage |
| get_ncbi_synonyms | Get NCBI synonyms |
| get_ncbi_taxonomy | Download NCBI taxdump |
| get_ott_lineage | Recursively get lineage from OTT taxid This function derives... |
| get_ott_taxonomy | get_ott_taxonomy |
| get_reading_frame | Get Reading frame of sequences |
| get_subalignment | Get subalignment |
| gid_to_acc | Convert NCBI gene ids to accession numbers |
| graft_tips | Graft new tips onto an existing tree |
| hex2acc | Hexadecimal coding to accession numberD |
| kmer_screen | Kmer screening function |
| lca_probs | Probabilitys of sharing a rank as a function of sequence... |
| makeblastdb | Make blast Database (DEPRECATED) |
| make_blast_db | Make blast Database |
| map_to_model | Map to model |
| map_to_ott | Map taxa to open tree of life |
| model | COI phmm model |
| ncbi_taxid | Get ncbi taxid's for a taxon name |
| pad_alignment | Pad alignment |
| parse_gb | Parse genbank flat files |
| parse_ott_synonyms | parse the open tree of life synonyms file |
| pipe | Pipe operator |
| propagate_tax | Propagate taxonomy (DEPRECATED) |
| prune_groups | Prune group sizes |
| random_seq | Generate random sequences |
| read_bold_chunk | read bold chunk |
| read_genbank_chunk | Read genbank chunk |
| reformat_dada2_gen | Reformat DADA2 Genus |
| reformat_dada2_spp | Reformat DADA2 Species |
| reformat_hierarchy | Reformat hierarchy |
| resolve_synonyms_ncbi | resolve_synonyms_ncbi |
| setup_multithread | Setup multithreading |
| setup_para | Setup parallel |
| split_bold_query | Split bold query This function recursively splits a bold... |
| subset_model | Subset PHMM Modified from Cameron Nugent's COIL package... |
| summarise_fasta | summarise_fasta |
| tax2phylo | tax2phylo |
| tax2tree | tax2tree |
| train_idtaxa | Train IDTAXA |
| write_fasta | write fasta |
