phyloseq-package	phyloseq-package
access	access
assign-otuTable	assign-otuTable
assign-sampleData	assign-sampleData
assign-speciesarerows	assign-speciesarerows
assign-taxTab	assign-taxTab
assign-tre	assign-tre
cca.phyloseq	cca-rda-phyloseq-methods
cca.phyloseq,formula-method	cca-rda-phyloseq-methods
cca.phyloseq,otuTable-method	cca-rda-phyloseq-methods
cca.phyloseq,phyloseq-method	cca-rda-phyloseq-methods
colname2hex	colname2hex
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
envHash2otuTable	envHash2otuTable
esophagus	data-esophagus
estimate_richness	estimate_richness
export_env_file	export_env_file
export_mothur_dist	export_mothur_dist
filterfunSample	filterfunSample
filter_taxa	filter_taxa
genefilterSample	genefilterSample-methods
genefilterSample,matrix-method	genefilterSample-methods
genefilterSample,otuTable-method	genefilterSample-methods
genefilterSample,phyloseq-method	genefilterSample-methods
get.component.classes	get.component.classes
getSamples	getSamples-methods
getSamples,otuTable-method	getSamples-methods
getSamples,phyloseq-method	getSamples-methods
getslots.phyloseq	getslots.phyloseq
getSpecies	getSpecies-methods
getSpecies,otuTable-method	getSpecies-methods
getSpecies,phyloseq-method	getSpecies-methods
getTaxa	getTaxa
getTipDistMatrix	getTipDistMatrix
gettipdistmatrix	getTipDistMatrix
getVariable	getVariable
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_otutable	import_mothur_otutable
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_sampleData
import_RDP_cluster	import_RDP_cluster
internal2tips.self	internal2tips.self
intersect_species	intersect_species
JSD	JSD
make_sample_network	make_sample_network
merge_phyloseq	merge_phyloseq
merge_phyloseq_pair	merge_phyloseq_pair-methods
merge_phyloseq_pair,otuTable,otuTable-method	merge_phyloseq_pair-methods
merge_phyloseq_pair,phylo,phylo-method	merge_phyloseq_pair-methods
merge_phyloseq_pair,sampleData,sampleData-method	merge_phyloseq_pair-methods
merge_phyloseq_pair,taxonomyTable,taxonomyTable-method	merge_phyloseq_pair-methods
merge_samples	merge_samples-methods
merge_samples,otuTable-method	merge_samples-methods
merge_samples,phyloseq-method	merge_samples-methods
merge_samples,sampleData-method	merge_samples-methods
merge_species	merge_species-methods
merge_species,otuTable-method	merge_species-methods
merge_species,phylo-method	merge_species-methods
merge_species,phyloseq-method	merge_species-methods
merge_species,sampleData-method	merge_species-methods
merge_species,taxonomyTable-method	merge_species-methods
mt	mt-methods
mt,otuTable,character-method	mt-methods
mt,otuTable,factor-method	mt-methods
mt,otuTable,integer-method	mt-methods
mt,otuTable,logical-method	mt-methods
mt,otuTable,numeric-method	mt-methods
mt,phyloseq,ANY-method	mt-methods
nsamples	nsamples-methods
nsamples,ANY-method	nsamples-methods
nsamples,otuTable-method	nsamples-methods
nsamples,phyloseq-method	nsamples-methods
nsamples,sampleData-method	nsamples-methods
nspecies	nspecies-methods
nspecies,ANY-method	nspecies-methods
nspecies,otuTable-method	nspecies-methods
nspecies,phylo-method	nspecies-methods
nspecies,phyloseq-method	nspecies-methods
nspecies,taxonomyTable-method	nspecies-methods
ordinate	ordinate
otu2df	otu2df
otuTable	otuTable-methods
otuTable,data.frame-method	otuTable-methods
otuTable,matrix-method	otuTable-methods
otuTable,otuTable-method	otuTable-methods
otuTable,phyloseq-method	otuTable-methods
otuTable-class	otuTable-class
otuTable<-	assign-otuTable
otuTable<-,otuTable,otuTable-method	assign-otuTable
otuTable<-,phyloseq,otuTable-method	assign-otuTable
otuTable<-,phyloseq,phyloseq-method	assign-otuTable
phylo-class	phylo-class
phyloseq	phyloseq
phyloseq-class	phyloseq-class
plot_ordination	plot_ordination
plot_phyloseq	plot_phyloseq-methods
plot_phyloseq,phyloseq-method	plot_phyloseq-methods
plot_richness_estimates	plot_richness_estimates
plot_sample_network	plot_sample_network
plot_taxa_bar	plot-taxa-bar
plot_tree_phyloseq	plot_tree_phyloseq
prune_samples	prune_samples-methods
prune_samples,character,otuTable-method	prune_samples-methods
prune_samples,character,phyloseq-method	prune_samples-methods
prune_samples,character,sampleData-method	prune_samples-methods
prune_species	prune_species-methods
prune_species,character,otuTable-method	prune_species-methods
prune_species,character,phylo-method	prune_species-methods
prune_species,character,phyloseq-method	prune_species-methods
prune_species,character,sampleData-method	prune_species-methods
prune_species,character,taxonomyTable-method	prune_species-methods
prune_species,logical,ANY-method	prune_species-methods
prune_species,NULL,ANY-method	prune_species-methods
rank.names	rank.names
rda.phyloseq	cca-rda-phyloseq-methods
rda.phyloseq,formula-method	cca-rda-phyloseq-methods
rda.phyloseq,otuTable-method	cca-rda-phyloseq-methods
rda.phyloseq,phyloseq-method	cca-rda-phyloseq-methods
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	sampleData-methods
samData<-	assign-sampleData
sample.names	sample.names-methods
sample.names,ANY-method	sample.names-methods
sample.names,otuTable-method	sample.names-methods
sample.names,phyloseq-method	sample.names-methods
sample.names,sampleData-method	sample.names-methods
sample.variables	sample.variables
sampleData	sampleData-methods
sampleData,ANY-method	sampleData-methods
sampleData,data.frame-method	sampleData-methods
sampleData-class	sampleData-class
sampleData<-	assign-sampleData
sampleMap	sampleData-methods
sampleNames	sample.names-methods
sampleSums	sampleSums
show	show-methods
show,otuTable-method	show-methods
show,phyloseq-method	show-methods
show,sampleData-method	show-methods
show,taxonomyTable-method	show-methods
show_mothur_list_cutoffs	show_mothur_list_cutoffs
soilrep	data-soilrep
species.names	species.names-methods
species.names,ANY-method	species.names-methods
species.names,otuTable-method	species.names-methods
species.names,phylo-method	species.names-methods
species.names,phyloseq-method	species.names-methods
species.names,sampleData-method	species.names-methods
species.names,taxonomyTable-method	species.names-methods
speciesAreRows	speciesAreRows-methods
speciesarerows	speciesAreRows-methods
speciesAreRows,ANY-method	speciesAreRows-methods
speciesAreRows,otuTable-method	speciesAreRows-methods
speciesAreRows,phyloseq-method	speciesAreRows-methods
speciesarerows<-	assign-speciesarerows
speciesarerows<-,otuTable,logical-method	assign-speciesarerows
speciesarerows<-,phyloseq,logical-method	assign-speciesarerows
speciesSums	speciesSums
splat.phyloseq.objects	splat.phyloseq.objects
subset_ord_plot	subset_ord_plot
subset_samples	subset_samples-methods
subset_species	subset_species-methods
t	transpose-methods
t,otuTable-method	transpose-methods
t,phyloseq-method	transpose-methods
taxaplot	plot-taxa-bar
taxglom	taxglom-methods
taxglom,otuTable,character-method	taxglom-methods
taxglom,otuTable,taxonomyTable-method	taxglom-methods
taxglom,phyloseq,ANY-method	taxglom-methods
taxglom.internal	taxglom.internal
taxonomyTable-class	taxonomyTable-class
taxTab	taxTab-methods
taxtab	taxTab-methods
taxTab,ANY-method	taxTab-methods
taxTab,matrix-method	taxTab-methods
taxTab<-	assign-taxTab
threshrank	threshrank
threshrankfun	threshrankfun
tipglom	tipglom-methods
tipglom,phylo,ANY-method	tipglom-methods
tipglom,phylo,otuTable-method	tipglom-methods
tipglom,phyloseq,ANY-method	tipglom-methods
tipglom.internal	tipglom.internal
tipsymbols	tip-annotate
tiptext	tip-annotate
topf	topf
topk	topk
topp	topp
TransformSampleCounts	transformcounts
transformSampleCounts	transformcounts
transformsamplecounts	transformcounts
tre	tre-methods
tre,ANY-method	tre-methods
tre,phylo-method	tre-methods
tre<-	assign-tre
tre<-,phyloseq,phylo-method	assign-tre
tre<-,phyloseq,phyloseq-method	assign-tre
ufnum	ufnum
UFwi	UFwi
UniFrac	UniFrac-methods
UniFrac,phyloseq-method	UniFrac-methods
unifracPair	unifracPair
wUniFracPair	wUniFracPair
[	extract-methods
[,otuTable-method	extract-methods
[,phyloseq-method	extract-methods
[,sampleData-method	extract-methods
[,taxonomyTable-method	extract-methods
