phyloseq-package	phyloseq-package
access	access
assign-otu_table	assign-otu_table
assign-phy_tree	assign-phy_tree
assign-sample_data	assign-sample_data
assign-taxa_are_rows	assign-taxa_are_rows
assign-tax_table	assign-tax_table
cca.phyloseq	cca-rda-phyloseq-methods
cca.phyloseq,formula-method	cca-rda-phyloseq-methods
cca.phyloseq,otu_table-method	cca-rda-phyloseq-methods
cca.phyloseq,phyloseq-method	cca-rda-phyloseq-methods
data-enterotype	data-enterotype
data-esophagus	data-esophagus
data-GlobalPatterns	data-GlobalPatterns
data-soilrep	data-soilrep
distance	distance
DPCoA	DPCoA
edgelist2clique	edgelist2clique
enterotype	data-enterotype
envHash2otu_table	envHash2otu_table
esophagus	data-esophagus
estimate_richness	estimate_richness
export_env_file	export_env_file
export_mothur_dist	export_mothur_dist
filterfunSample	filterfun_sample
filterfun_sample	filterfun_sample
filter_taxa	filter_taxa
genefilterSample	genefilter_sample-methods
genefilter_sample	genefilter_sample-methods
genefilter_sample,matrix-method	genefilter_sample-methods
genefilter_sample,otu_table-method	genefilter_sample-methods
genefilter_sample,phyloseq-method	genefilter_sample-methods
get.component.classes	get.component.classes
getSamples	get_sample-methods
getslots.phyloseq	getslots.phyloseq
getSpecies	get_taxa-methods
getTaxa	get_taxa_unique
getTipDistMatrix	getTipDistMatrix
gettipdistmatrix	getTipDistMatrix
getVariable	get_variable
get_sample	get_sample-methods
get_sample,otu_table-method	get_sample-methods
get_sample,phyloseq-method	get_sample-methods
get_taxa	get_taxa-methods
get_taxa,otu_table-method	get_taxa-methods
get_taxa,phyloseq-method	get_taxa-methods
get_taxa_unique	get_taxa_unique
get_variable	get_variable
GlobalPatterns	data-GlobalPatterns
import	import
import_biom	import_biom
import_env_file	import_env_file
import_mothur	import_mothur
import_mothur_dist	import_mothur_dist
import_mothur_groups	import_mothur_groups
import_mothur_otulist	import_mothur_otulist
import_mothur_otu_table	import_mothur_otu_table
import_mothur_tree	import_mothur_tree
import_pyrotagger_tab	import_pyrotagger_tab
import_qiime	import_qiime
import_qiime_otu_tax	import_qiime_otu_tax
import_qiime_sampleData	import_qiime_sample_data
import_qiime_sample_data	import_qiime_sample_data
import_RDP_cluster	import_RDP_cluster
import_RDP_otu	import_RDP_otu
internal2tips.self	internal2tips.self
intersect_species	intersect_species
JSD	JSD
make_network	make_network
merge_phyloseq	merge_phyloseq
merge_phyloseq_pair	merge_phyloseq_pair-methods
merge_phyloseq_pair,otu_table,otu_table-method	merge_phyloseq_pair-methods
merge_phyloseq_pair,phylo,phylo-method	merge_phyloseq_pair-methods
merge_phyloseq_pair,sample_data,sample_data-method	merge_phyloseq_pair-methods
merge_phyloseq_pair,taxonomyTable,taxonomyTable-method	merge_phyloseq_pair-methods
merge_samples	merge_samples-methods
merge_samples,otu_table-method	merge_samples-methods
merge_samples,phyloseq-method	merge_samples-methods
merge_samples,sample_data-method	merge_samples-methods
merge_species	merge_taxa-methods
merge_taxa	merge_taxa-methods
merge_taxa,otu_table-method	merge_taxa-methods
merge_taxa,phylo-method	merge_taxa-methods
merge_taxa,phyloseq-method	merge_taxa-methods
merge_taxa,sample_data-method	merge_taxa-methods
merge_taxa,taxonomyTable-method	merge_taxa-methods
mt	mt-methods
mt,otu_table,character-method	mt-methods
mt,otu_table,factor-method	mt-methods
mt,otu_table,integer-method	mt-methods
mt,otu_table,logical-method	mt-methods
mt,otu_table,numeric-method	mt-methods
mt,phyloseq,ANY-method	mt-methods
nsamples	nsamples-methods
nsamples,ANY-method	nsamples-methods
nsamples,otu_table-method	nsamples-methods
nsamples,phyloseq-method	nsamples-methods
nsamples,sample_data-method	nsamples-methods
nspecies	ntaxa-methods
ntaxa	ntaxa-methods
ntaxa,ANY-method	ntaxa-methods
ntaxa,otu_table-method	ntaxa-methods
ntaxa,phylo-method	ntaxa-methods
ntaxa,phyloseq-method	ntaxa-methods
ntaxa,taxonomyTable-method	ntaxa-methods
ordinate	ordinate
otu2df	otu2df
otuTable	otu_table-methods
otuTable<-	assign-otu_table
otu_table	otu_table-methods
otu_table,data.frame-method	otu_table-methods
otu_table,matrix-method	otu_table-methods
otu_table,otu_table-method	otu_table-methods
otu_table,phyloseq-method	otu_table-methods
otu_table-class	otu_table-class
otu_table<-	assign-otu_table
otu_table<-,otu_table,otu_table-method	assign-otu_table
otu_table<-,phyloseq,otu_table-method	assign-otu_table
otu_table<-,phyloseq,phyloseq-method	assign-otu_table
phylo-class	phylo-class
phyloseq	phyloseq
phyloseq-class	phyloseq-class
phy_tree	phy_tree-methods
phy_tree,ANY-method	phy_tree-methods
phy_tree,phylo-method	phy_tree-methods
phy_tree<-	assign-phy_tree
phy_tree<-,phyloseq,phylo-method	assign-phy_tree
phy_tree<-,phyloseq,phyloseq-method	assign-phy_tree
plot_heatmap	plot_heatmap
plot_network	plot_network
plot_ordination	plot_ordination
plot_phyloseq	plot_phyloseq-methods
plot_phyloseq,phyloseq-method	plot_phyloseq-methods
plot_richness	plot_richness
plot_richness_estimates	plot_richness
plot_taxa_bar	plot-taxa-bar
plot_tree	plot_tree
prune_samples	prune_samples-methods
prune_samples,character,otu_table-method	prune_samples-methods
prune_samples,character,phyloseq-method	prune_samples-methods
prune_samples,character,sample_data-method	prune_samples-methods
prune_samples,logical,ANY-method	prune_samples-methods
prune_species	prune_taxa-methods
prune_taxa	prune_taxa-methods
prune_taxa,character,otu_table-method	prune_taxa-methods
prune_taxa,character,phylo-method	prune_taxa-methods
prune_taxa,character,phyloseq-method	prune_taxa-methods
prune_taxa,character,sample_data-method	prune_taxa-methods
prune_taxa,character,taxonomyTable-method	prune_taxa-methods
prune_taxa,logical,ANY-method	prune_taxa-methods
prune_taxa,NULL,ANY-method	prune_taxa-methods
rank.names	rank_names
rank_names	rank_names
rarefy_even_depth	rarefy_even_depth
rda.phyloseq	cca-rda-phyloseq-methods
rda.phyloseq,formula-method	cca-rda-phyloseq-methods
rda.phyloseq,otu_table-method	cca-rda-phyloseq-methods
rda.phyloseq,phyloseq-method	cca-rda-phyloseq-methods
read_tree	read_tree
reconcile_categories	reconcile_categories
reconcile_samples	reconcile_samples
reconcile_species	reconcile_species-methods
reconcile_species,phyloseq-method	reconcile_species-methods
rm_outlierf	rm_outlierf
samData	sample_data-methods
sample.names	sample_names-methods
sample.variables	sample_variables
sampleData	sample_data-methods
sampleData<-	assign-sample_data
sampleNames	sample_names-methods
sampleSums	sample_sums
sample_data	sample_data-methods
sample_data,ANY-method	sample_data-methods
sample_data,data.frame-method	sample_data-methods
sample_data-class	sample_data-class
sample_data<-	assign-sample_data
sample_names	sample_names-methods
sample_names,ANY-method	sample_names-methods
sample_names,otu_table-method	sample_names-methods
sample_names,phyloseq-method	sample_names-methods
sample_names,sample_data-method	sample_names-methods
sample_sums	sample_sums
sample_variables	sample_variables
sam_data	sample_data-methods
sam_data<-	assign-sample_data
show	show-methods
show,otu_table-method	show-methods
show,phyloseq-method	show-methods
show,sample_data-method	show-methods
show,taxonomyTable-method	show-methods
show_mothur_list_cutoffs	show_mothur_list_cutoffs
soilrep	data-soilrep
species.names	taxa_names-methods
speciesAreRows	taxa_are_rows-methods
speciesarerows	taxa_are_rows-methods
speciesAreRows<-	assign-taxa_are_rows
speciesSums	taxa_sums
splat.phyloseq.objects	splat.phyloseq.objects
subset_ord_plot	subset_ord_plot
subset_samples	subset_samples-methods
subset_species	subset_taxa-methods
subset_taxa	subset_taxa-methods
t	transpose-methods
t,otu_table-method	transpose-methods
t,phyloseq-method	transpose-methods
tags.into.df	tags.into.df
taxaplot	plot-taxa-bar
taxa_are_rows	taxa_are_rows-methods
taxa_are_rows,ANY-method	taxa_are_rows-methods
taxa_are_rows,otu_table-method	taxa_are_rows-methods
taxa_are_rows,phyloseq-method	taxa_are_rows-methods
taxa_are_rows<-	assign-taxa_are_rows
taxa_are_rows<-,otu_table,logical-method	assign-taxa_are_rows
taxa_are_rows<-,phyloseq,logical-method	assign-taxa_are_rows
taxa_names	taxa_names-methods
taxa_names,ANY-method	taxa_names-methods
taxa_names,otu_table-method	taxa_names-methods
taxa_names,phylo-method	taxa_names-methods
taxa_names,phyloseq-method	taxa_names-methods
taxa_names,sample_data-method	taxa_names-methods
taxa_names,taxonomyTable-method	taxa_names-methods
taxa_sums	taxa_sums
taxglom	tax_glom
taxonomyTable-class	taxonomyTable-class
taxTab	tax_table-methods
taxtab	tax_table-methods
taxTab<-	assign-tax_table
tax_glom	tax_glom
tax_table	tax_table-methods
tax_table,ANY-method	tax_table-methods
tax_table,data.frame-method	tax_table-methods
tax_table,matrix-method	tax_table-methods
tax_table<-	assign-tax_table
tax_table<-,phyloseq,ANY-method	assign-tax_table
tax_table<-,phyloseq,taxonomyTable-method	assign-tax_table
tax_table<-,taxonomyTable,ANY-method	assign-tax_table
tax_table<-,taxonomyTable,taxonomyTable-method	assign-tax_table
threshrank	threshrank
threshrankfun	threshrankfun
tipglom	tip_glom-methods
tip_glom	tip_glom-methods
tip_glom,phylo,ANY-method	tip_glom-methods
tip_glom,phylo,otu_table-method	tip_glom-methods
tip_glom,phyloseq,ANY-method	tip_glom-methods
tip_glom.internal	tip_glom.internal
topf	topf
topk	topk
topp	topp
transformSampleCounts	transformcounts
transform_sample_counts	transformcounts
tre	phy_tree-methods
tre<-	assign-phy_tree
tree.branch.length	tree.branch.length
tree.child.nodes	tree.child.nodes
tree.get.tags	tree.get.tags
tree.has.tags	tree.has.tags
tree.layout	tree.layout
tree.length.to.root	tree.length.to.root
tree.parent.node	tree.parent.node
ufnum	ufnum
UFwi	UFwi
UniFrac	UniFrac-methods
UniFrac,phyloseq-method	UniFrac-methods
unifracPair	unifracPair
wUniFracPair	wUniFracPair
[	extract-methods
[,otu_table-method	extract-methods
[,phyloseq-method	extract-methods
[,sample_data-method	extract-methods
[,taxonomyTable-method	extract-methods
