as_phyloseq             Convert taxmap to phyloseq
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
compare_groups          Compare groups of samples
complement              Find complement of sequences
counts_to_presence      Apply a function to groups of columns
diverging_palette       The default diverging color palette
filter_ambiguous_taxa   Filter ambiguous taxon names
heat_tree               Plot a taxonomic tree
heat_tree_matrix        Plot a matrix of heat trees
hmp_otus                A HMP subset
hmp_samples             Sample information for HMP subset
is_ambiguous            Find ambiguous taxon names
layout_functions        Layout functions
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
metacoder               Metacoder
ncbi_taxon_sample       Download representative sequences for a 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_qiime_biom        Parse a BIOM output from QIIME
parse_rdp               Parse RDP FASTA release
parse_silva_fasta       Parse SILVA FASTA release
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
qualitative_palette     The default qualitative color palette
quantative_palette      The default quantative color palette
rarefy_obs              Calculate rarefied observation counts
read_fasta              Read a FASTA file
rev_comp                Revere complement sequences
reverse                 Reverse sequences
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
