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
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
extract_tax_data        Extracts taxonomy info from vectors with regex
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
filtering-helpers       Taxonomic filtering helpers
get_data                Get data in a taxmap object by name
get_data_frame          Get data in a taxonomy or taxmap object by name
get_dataset             Get a data set from a taxmap object
heat_tree               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
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
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
ncbi_taxon_sample       Download representative sequences for a taxon
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_tax_summary
                        Parse mothur *.tax.summary Classify.seqs output
parse_mothur_taxonomy   Parse mothur Classify.seqs *.taxonomy 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_is_installed
                        Test if primersearch is installed
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_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
rev_comp                Revere complement sequences
reverse                 Reverse 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
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
taxonomy                Taxonomy class
taxonomy_table          Convert taxonomy info to a table
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
