A B C D E F G H I L M N O P Q R S T W Z
| taxa-package | taxa |
| all_names | Return names of data in [taxonomy()] or [taxmap()] |
| ambiguous_synonyms | Get patterns for ambiguous taxa |
| arrange_obs | Sort user data in [taxmap()] objects |
| arrange_taxa | Sort the edge list of [taxmap()] objects |
| as_phyloseq | Convert taxmap to phyloseq |
| branches | Get "branch" taxa |
| calc_diff_abund_deseq2 | Differential abundance with DESeq2 |
| calc_group_mean | Calculate means of groups of columns |
| calc_group_median | Calculate medians of groups of columns |
| calc_group_rsd | Relative standard deviations of groups of columns |
| calc_group_stat | Apply a function to groups of columns |
| calc_n_samples | Count the number of samples |
| calc_obs_props | Calculate proportions from observation counts |
| calc_prop_samples | Calculate the proportion of samples |
| classifications | Get classifications of taxa |
| compare_groups | Compare groups of samples |
| complement | Find complement of sequences |
| counts_to_presence | Apply a function to groups of columns |
| database_list | Database list |
| diverging_palette | The default diverging color palette |
| extract_tax_data | Extracts taxonomy info from vectors with regex |
| ex_hierarchies | An example hierarchies object |
| ex_hierarchy1 | An example Hierarchy object |
| ex_hierarchy2 | An example Hierarchy object |
| ex_hierarchy3 | An example Hierarchy object |
| ex_taxmap | An example taxmap object |
| filtering-helpers | Taxonomic filtering helpers |
| filter_ambiguous_taxa | Filter ambiguous taxon names |
| filter_obs | Filter observations with a list of conditions |
| filter_taxa | Filter taxa with a list of conditions |
| get_data | Get data in a taxmap object by name |
| get_dataset | Get a data set from a taxmap object |
| get_data_frame | Get data in a taxonomy or taxmap object by name |
| heat_tree | Plot a taxonomic tree |
| heat_tree.default | Plot a taxonomic tree |
| heat_tree.Taxmap | Plot a taxonomic tree |
| heat_tree_matrix | Plot a matrix of heat trees |
| hierarchies | Make a set of many [hierarchy()] class objects |
| hierarchy | The Hierarchy class |
| highlight_taxon_ids | Highlight taxon ID column |
| hmp_otus | A HMP subset |
| hmp_samples | Sample information for HMP subset |
| ids | Taxonomic filtering helpers |
| id_classifications | Get ID classifications of taxa |
| internodes | Get "internode" taxa |
| is_ambiguous | Find ambiguous taxon names |
| is_branch | Test if taxa are branches |
| is_internode | Test if taxa are "internodes" |
| is_leaf | Test if taxa are leaves |
| is_root | Test if taxa are roots |
| is_stem | Test if taxa are stems |
| layout_functions | Layout functions |
| leaves | Get leaf taxa |
| leaves_apply | Apply function to leaves of each taxon |
| lookup_tax_data | Convert one or more data sets to taxmap |
| make_dada2_asv_table | Make a imitation of the dada2 ASV abundance matrix |
| make_dada2_tax_table | Make a imitation of the dada2 taxonomy matrix |
| map_data | Create a mapping between two variables |
| map_data_ | Create a mapping without NSE |
| metacoder | Metacoder |
| mutate_obs | Add columns to [taxmap()] objects |
| ncbi_taxon_sample | Download representative sequences for a taxon |
| nms | Taxonomic filtering helpers |
| n_leaves | Get number of leaves |
| n_leaves_1 | Get number of leaves |
| n_obs | Count observations in [taxmap()] |
| n_obs_1 | Count observation assigned in [taxmap()] |
| n_subtaxa | Get number of subtaxa |
| n_subtaxa_1 | Get number of subtaxa |
| n_supertaxa | Get number of supertaxa |
| n_supertaxa_1 | Get number of supertaxa |
| obs | Get data indexes associated with taxa |
| obs_apply | Apply function to observations per taxon |
| parse_dada2 | Convert the output of dada2 to a taxmap object |
| parse_greengenes | Parse Greengenes release |
| parse_mothur_taxonomy | Parse mothur Classify.seqs *.taxonomy output |
| parse_mothur_tax_summary | Parse mothur *.tax.summary Classify.seqs output |
| parse_newick | Parse a Newick file |
| parse_phylo | Parse a phylo object |
| parse_phyloseq | Convert a phyloseq to taxmap |
| parse_primersearch | Parse EMBOSS primersearch output |
| parse_qiime_biom | Parse a BIOM output from QIIME |
| parse_rdp | Parse RDP FASTA release |
| parse_silva_fasta | Parse SILVA FASTA release |
| parse_tax_data | Convert one or more data sets to taxmap |
| parse_ubiome | Converts the uBiome file format to taxmap |
| parse_unite_general | Parse UNITE general release FASTA |
| primersearch | Use EMBOSS primersearch for in silico PCR |
| primersearch_raw | Use EMBOSS primersearch for in silico PCR |
| print_tree | Print a text tree |
| qualitative_palette | The default qualitative color palette |
| quantative_palette | The default quantative color palette |
| ranks | Taxonomic filtering helpers |
| ranks_ref | Lookup-table for IDs of taxonomic ranks |
| rarefy_obs | Calculate rarefied observation counts |
| read_fasta | Read a FASTA file |
| remove_redundant_names | Remove redundant parts of taxon names |
| replace_taxon_ids | Replace taxon ids |
| reverse | Reverse sequences |
| rev_comp | Revere complement sequences |
| roots | Get root taxa |
| sample_frac_obs | Sample a proportion of observations from [taxmap()] |
| sample_frac_taxa | Sample a proportion of taxa from [taxonomy()] or [taxmap()] |
| sample_n_obs | Sample n observations from [taxmap()] |
| sample_n_taxa | Sample n taxa from [taxonomy()] or [taxmap()] |
| select_obs | Subset columns in a [taxmap()] object |
| stems | Get stem taxa |
| subtaxa | Get subtaxa |
| subtaxa_apply | Apply function to subtaxa of each taxon |
| supertaxa | Get all supertaxa of a taxon |
| supertaxa_apply | Apply function to supertaxa of each taxon |
| taxa | A class for multiple taxon objects |
| taxmap | Taxmap class |
| taxon | Taxon class |
| taxonomy | Taxonomy class |
| taxonomy_table | Convert taxonomy info to a table |
| taxon_database | Taxonomy database class |
| taxon_id | Taxon ID class |
| taxon_ids | Get taxon IDs |
| taxon_indexes | Get taxon indexes |
| taxon_name | Taxon name class |
| taxon_names | Get taxon names |
| taxon_rank | Taxon rank class |
| taxon_ranks | Get taxon ranks |
| transmute_obs | Replace columns in [taxmap()] objects |
| write_greengenes | Write an imitation of the Greengenes database |
| write_mothur_taxonomy | Write an imitation of the Mothur taxonomy file |
| write_rdp | Write an imitation of the RDP FASTA database |
| write_silva_fasta | Write an imitation of the SILVA FASTA database |
| write_unite_general | Write an imitation of the UNITE general FASTA database |
| zero_low_counts | Replace low counts with zero |