taxa-package	taxa-package
%>%	grapes-greater-than-grapes
.onAttach	dot-onAttach
add_alpha	add_alpha
all_functions	all_functions
all_names	all_names
ambiguous_patterns	ambiguous_patterns
ambiguous_synonyms	ambiguous_synonyms
apply_color_scale	apply_color_scale
arrange_obs	arrange_obs
arrange_taxa	arrange_taxa
as_id	as_id
as_phyloseq	as_phyloseq
branches	branches
calc_diff_abund_deseq2	calc_diff_abund_deseq2
calc_group_mean	calc_group_mean
calc_group_median	calc_group_median
calc_group_rsd	calc_group_rsd
calc_group_stat	calc_group_stat
calc_n_samples	calc_n_samples
calc_obs_props	calc_obs_props
calc_prop_samples	calc_prop_samples
calc_taxon_abund	calc_taxon_abund
can_be_num	can_be_num
can_be_used_in_taxmap	can_be_used_in_taxmap
capitalize	capitalize
check_class_col	check_class_col
check_element_length	check_element_length
check_for_pkg	check_for_pkg
check_option_groups	check_option_groups
check_taxmap_data	check_taxmap_data
classifications	classifications
compare_groups	compare_groups
complement	complement
contains	contains
convert_base	convert_base
correct_taxon_names	correct_taxon_names
counts_to_presence	counts_to_presence
count_capture_groups	count_capture_groups
database_list	database_list
data_used	data_used
desc_font	desc_font
diverging_palette	diverging_palette
DNAbin_to_char	DNAbin_to_char
do_calc_on_num_cols	do_calc_on_num_cols
edge_list_depth	edge_list_depth
ends_with	ends_with
error_font	error_font
everything	everything
extract_tax_data	extract_tax_data
ex_hierarchies	ex_hierarchies
ex_hierarchy1	ex_hierarchy1
ex_hierarchy2	ex_hierarchy2
ex_hierarchy3	ex_hierarchy3
ex_taxmap	ex_taxmap
fasta_headers	fasta_headers
filtering-helpers	filtering-helpers
filter_ambiguous_taxa	filter_ambiguous_taxa
filter_obs	filter_obs
filter_taxa	filter_taxa
get_class_from_el	get_class_from_el
get_data	get_data
get_database_name	get_database_name
get_dataset	get_dataset
get_data_frame	get_data_frame
get_dots_or_list	get_dots_or_list
get_edge_children	get_edge_children
get_edge_parents	get_edge_parents
get_expected_data	get_expected_data
get_node_children	get_node_children
get_numerics	get_numerics
get_numeric_cols	get_numeric_cols
get_optimal_range	get_optimal_range
get_sort_var	get_sort_var
get_taxmap_cols	get_taxmap_cols
get_taxmap_data	get_taxmap_data
get_taxmap_other_cols	get_taxmap_other_cols
get_taxmap_table	get_taxmap_table
get_taxonomy_levels	get_taxonomy_levels
heat_tree	heat_tree
heat_tree.default	heat_tree
heat_tree.Taxmap	heat_tree
heat_tree_matrix	heat_tree_matrix
hierarchies	hierarchies
hierarchy	hierarchy
highlight_taxon_ids	highlight_taxon_ids
hmp_otus	hmp_otus
hmp_samples	hmp_samples
ids	filtering-helpers
id_classifications	id_classifications
init_taxmap_data	init_taxmap_data
internodes	internodes
inter_circle_gap	inter_circle_gap
inverse	inverse
is_ambiguous	is_ambiguous
is_branch	is_branch
is_internode	is_internode
is_leaf	is_leaf
is_root	is_root
is_stem	is_stem
label_bounds	label_bounds
layout_functions	layout_functions
leaves	leaves
leaves_apply	leaves_apply
length_of_thing	length_of_thing
limited_print	limited_print
line_coords	line_coords
lookup_tax_data	lookup_tax_data
look_for_na	look_for_na
make_dada2_asv_table	make_dada2_asv_table
make_dada2_tax_table	make_dada2_tax_table
make_fasta_with_u_replaced	make_fasta_with_u_replaced
make_plot_legend	make_plot_legend
map_data	map_data
map_data_	map_data_
map_unique	map_unique
matches	matches
metacoder	metacoder
molten_dist	molten_dist
multi_sep_split	multi_sep_split
mutate_obs	mutate_obs
my_print	my_print
names_used	names_used
name_font	name_font
ncbi_sequence	ncbi_sequence
ncbi_taxon_sample	ncbi_taxon_sample
nms	filtering-helpers
num_range	num_range
n_leaves	n_leaves
n_leaves_1	n_leaves_1
n_obs	n_obs
n_obs_1	n_obs_1
n_subtaxa	n_subtaxa
n_subtaxa_1	n_subtaxa_1
n_supertaxa	n_supertaxa
n_supertaxa_1	n_supertaxa_1
obs	obs
obs_apply	obs_apply
one_of	one_of
parse_dada2	parse_dada2
parse_dataset	parse_dataset
parse_edge_list	parse_edge_list
parse_greengenes	parse_greengenes
parse_heirarchies_to_taxonomy	parse_heirarchies_to_taxonomy
parse_mothur_taxonomy	parse_mothur_taxonomy
parse_mothur_tax_summary	parse_mothur_tax_summary
parse_newick	parse_newick
parse_phylo	parse_phylo
parse_phyloseq	parse_phyloseq
parse_possibly_named_logical	parse_possibly_named_logical
parse_primersearch	parse_primersearch
parse_qiime_biom	parse_qiime_biom
parse_raw_heirarchies_to_taxonomy	parse_raw_heirarchies_to_taxonomy
parse_rdp	parse_rdp
parse_seq_input	parse_seq_input
parse_silva_fasta	parse_silva_fasta
parse_summary_seqs	parse_summary_seqs
parse_tax_data	parse_tax_data
parse_ubiome	parse_ubiome
parse_unite_general	parse_unite_general
polygon_coords	polygon_coords
prefixed_print	prefixed_print
primersearch	primersearch
primersearch_is_installed	primersearch_is_installed
primersearch_raw	primersearch_raw
print_item	print_item
print_tree	print_tree
print__character	print__character
print__data.frame	print__data.frame
print__default_	print__default_
print__factor	print__factor
print__integer	print__integer
print__list	print__list
print__logical	print__logical
print__matrix	print__matrix
print__numeric	print__numeric
print__ordered	print__ordered
print__tbl_df	print__tbl_df
print__vector	print__vector
progress_lapply	progress_lapply
punc_font	punc_font
qualitative_palette	qualitative_palette
quantative_palette	quantative_palette
ranks	filtering-helpers
ranks_ref	ranks_ref
rarefy_obs	rarefy_obs
read_fasta	read_fasta
read_lines_apply	read_lines_apply
remove_redundant_names	remove_redundant_names
replace_taxon_ids	replace_taxon_ids
repo_url	repo_url
rescale	rescale
reverse	reverse
rev_comp	rev_comp
roots	roots
run_primersearch	run_primersearch
sample_frac_obs	sample_frac_obs
sample_frac_taxa	sample_frac_taxa
sample_n_obs	sample_n_obs
sample_n_taxa	sample_n_taxa
scale_bar_coords	scale_bar_coords
select_labels	select_labels
select_obs	select_obs
simplify	simplify
split_by_level	split_by_level
starts_with	starts_with
startup_msg	startup_msg
stems	stems
subtaxa	subtaxa
subtaxa_apply	subtaxa_apply
supertaxa	supertaxa
supertaxa_apply	supertaxa_apply
taxa	taxa
taxmap	taxmap
taxon	taxon
taxonomy	taxonomy
taxonomy_table	taxonomy_table
taxon_database	taxon_database
taxon_id	taxon_id
taxon_ids	taxon_ids
taxon_indexes	taxon_indexes
taxon_name	taxon_name
taxon_names	taxon_names
taxon_rank	taxon_rank
taxon_ranks	taxon_ranks
text_grob_length	text_grob_length
tid_font	tid_font
to_percent	to_percent
transform_data	transform_data
transmute_obs	transmute_obs
unique_mapping	unique_mapping
validate_regex_key_pair	validate_regex_key_pair
validate_regex_match	validate_regex_match
validate_taxmap_funcs	validate_taxmap_funcs
verify_color_range	verify_color_range
verify_label_count	verify_label_count
verify_size	verify_size
verify_size_range	verify_size_range
verify_taxmap	verify_taxmap
verify_trans	verify_trans
write_greengenes	write_greengenes
write_mothur_taxonomy	write_mothur_taxonomy
write_rdp	write_rdp
write_silva_fasta	write_silva_fasta
write_unite_general	write_unite_general
zero_low_counts	zero_low_counts
