Geographically-Conscious Taxonomic Assignment for Metabarcoding
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Documentation for package ‘LocaTT’ version 1.1.1
Help Pages
| binomial_test | Binomial Test |
| blast_command_found | Check BLAST Installation |
| blast_version | Get BLAST Version |
| contains_wildcards | Check Whether DNA Sequences Contain Wildcard Characters |
| decode_quality_scores | Decode DNA Sequence Quality Scores |
| format_reference_database | Format Reference Databases |
| get_consensus_taxonomy | Get Consensus Taxonomy from Taxonomic Strings |
| get_taxonomic_level | Get Specified Taxonomic Level from Taxonomic Strings |
| get_taxonomies.IUCN | Get Taxonomies from IUCN Red List Files |
| get_taxonomies.species_binomials | Get NCBI Taxonomies from Species Binomials |
| isolate_amplicon | Trim DNA Sequences to an Amplicon Region Using Forward and Reverse Primer Sequences |
| local_taxa_tool | Perform Geographically-Conscious Taxonomic Assignment |
| merge_pairs | Merge Forward and Reverse DNA Sequence Reads |
| read.fasta | Read FASTA Files |
| read.fastq | Read FASTQ Files |
| reverse_complement | Get the Reverse Complement of a DNA Sequence |
| substitute_wildcards | Substitute Wildcard Characters in a DNA Sequence |
| trim_sequences | Trim Target Nucleotide Sequence from DNA Sequences |
| truncate_sequences.length | Truncate DNA Sequences to Specified Length |
| truncate_sequences.probability | Truncate DNA Sequences at Specified Probability that All Bases were Called Correctly |
| truncate_sequences.quality_score | Truncate DNA Sequences at Specified Quality Score |
| write.fasta | Write FASTA Files |
| write.fastq | Write FASTQ Files |