ambiguous_synonyms | Get patterns for ambiguous taxa |
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.default | Plot a taxonomic tree |
heat_tree.Taxmap | 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_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_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 |
reverse | Reverse sequences |
rev_comp | Revere complement 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 |