phyloseq-deprecated-package	phyloseq-deprecated
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-sample_names	assign-sample_names
assign-taxa_are_rows	assign-taxa_are_rows
assign-taxa_names	assign-taxa_names
assign-tax_table	assign-tax_table
build_tax_table	build_tax_table
capscale.phyloseq	capscale-phyloseq-methods
capscale.phyloseq,phyloseq,formula,character-method	capscale-phyloseq-methods
capscale.phyloseq,phyloseq,formula,dist-method	capscale-phyloseq-methods
cca.phyloseq	cca-rda-phyloseq-methods
cca.phyloseq,otu_table,ANY-method	cca-rda-phyloseq-methods
cca.phyloseq,otu_table-method	cca-rda-phyloseq-methods
cca.phyloseq,phyloseq,formula-method	cca-rda-phyloseq-methods
cca.phyloseq,phyloseq,NULL-method	cca-rda-phyloseq-methods
chunkReOrder	chunkReOrder
data-enterotype	data-enterotype
data-esophagus	data-esophagus
data-GlobalPatterns	data-GlobalPatterns
data-soilrep	data-soilrep
decorana	decorana
deprecated_phyloseq_function	phyloseq-deprecated
dist-class	dist-class
distance	distance
distance,otu_table,character-method	distance
distance,phyloseq,ANY-method	distance
distance,phyloseq,character-method	distance
distanceMethodList	distanceMethodList
DPCoA	DPCoA
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	phyloseq-deprecated
filterfun_sample	filterfun_sample
filter_taxa	filter_taxa
fix_phylo	fix_phylo
fix_phylo,phylo-method	fix_phylo
gapstat_ord	gapstat_ord
genefilterSample	phyloseq-deprecated
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	phyloseq-deprecated
getslots.phyloseq	getslots.phyloseq
getSpecies	phyloseq-deprecated
getTaxa	phyloseq-deprecated
getVariable	phyloseq-deprecated
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_constaxonomy	import_mothur_constaxonomy
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_shared	import_mothur_shared
import_pyrotagger_tab	import_pyrotagger_tab
import_qiime	import_qiime
import_qiime_otu_tax	import_qiime_otu_tax
import_qiime_sampleData	phyloseq-deprecated
import_qiime_sample_data	import_qiime_sample_data
import_RDP_cluster	import_RDP_cluster
import_RDP_otu	import_RDP_otu
import_uparse	import_uparse
import_usearch_uc	import_usearch_uc
index_reorder	index_reorder
index_reorder,phyloseq-method	index_reorder
intersect_taxa	intersect_taxa
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_phyloseq_pair,XStringSet,XStringSet-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	phyloseq-deprecated
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
merge_taxa,XStringSet-method	merge_taxa-methods
metaMDS	metaMDS
microbio_me_qiime	microbio_me_qiime
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
nodeplotblank	nodeplotblank
nodeplotboot	nodeplotboot
nodeplotdefault	nodeplotdefault
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	phyloseq-deprecated
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
ntaxa,XStringSet-method	ntaxa-methods
ordinate	ordinate
otuTable	phyloseq-deprecated
otuTable<-	phyloseq-deprecated
otu_table	otu_table-methods
otu_table,ANY-method	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
parse_taxonomy_default	parseTaxonomy-functions
parse_taxonomy_greengenes	parseTaxonomy-functions
parse_taxonomy_qiime	parseTaxonomy-functions
pcoa	pcoa
phylo	phylo
phylo-class	phylo-class
phyloseq	phyloseq
phyloseq-class	phyloseq-class
phyloseq-deprecated	phyloseq-deprecated
phyloseq_to_deseq2	phyloseq_to_deseq2
phyloseq_to_metagenomeSeq	phyloseq_to_metagenomeSeq
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_bar	plot_bar
plot_clusgap	plot_clusgap
plot_heatmap	plot_heatmap
plot_net	plot_net
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	phyloseq-deprecated
plot_scree	plot_scree
plot_taxa_bar	phyloseq-deprecated
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	phyloseq-deprecated
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,character,XStringSet-method	prune_taxa-methods
prune_taxa,logical,ANY-method	prune_taxa-methods
prune_taxa,NULL,ANY-method	prune_taxa-methods
psmelt	psmelt
rank.names	phyloseq-deprecated
rank_names	rank_names
rarefy_even_depth	rarefy_even_depth
rda.phyloseq	cca-rda-phyloseq-methods
read_tree	read_tree
read_tree_greengenes	read_tree_greengenes
reconcile_categories	reconcile_categories
refseq	refseq-methods
refseq,ANY-method	refseq-methods
refseq,XStringSet-method	refseq-methods
rm_outlierf	rm_outlierf
samData	phyloseq-deprecated
sample.names	phyloseq-deprecated
sample.variables	phyloseq-deprecated
sampleData	phyloseq-deprecated
sampleData<-	phyloseq-deprecated
sampleNames	phyloseq-deprecated
sampleSums	phyloseq-deprecated
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_names<-	assign-sample_names
sample_names<-,ANY,ANY-method	assign-sample_names
sample_names<-,ANY,character-method	assign-sample_names
sample_names<-,otu_table,character-method	assign-sample_names
sample_names<-,phyloseq,character-method	assign-sample_names
sample_names<-,sample_data,character-method	assign-sample_names
sample_sums	sample_sums
sample_variables	sample_variables
sam_data	phyloseq-deprecated
sam_data<-	phyloseq-deprecated
show,otu_table-method	show-methods
show,phyloseq-method	show-methods
show,sample_data-method	show-methods
show,taxonomyTable-method	show-methods
show_mothur_cutoffs	show_mothur_cutoffs
show_mothur_list_cutoffs	phyloseq-deprecated
soilrep	data-soilrep
species.names	phyloseq-deprecated
speciesAreRows	phyloseq-deprecated
speciesarerows	phyloseq-deprecated
speciesAreRows<-	phyloseq-deprecated
speciesSums	phyloseq-deprecated
splat.phyloseq.objects	splat.phyloseq.objects
subset_ord_plot	subset_ord_plot
subset_samples	subset_samples-methods
subset_species	phyloseq-deprecated
subset_taxa	subset_taxa-methods
t	transpose-methods
t,otu_table-method	transpose-methods
t,phyloseq-method	transpose-methods
taxaplot	phyloseq-deprecated
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_names,XStringSet-method	taxa_names-methods
taxa_names<-	assign-taxa_names
taxa_names<-,ANY,ANY-method	assign-taxa_names
taxa_names<-,ANY,character-method	assign-taxa_names
taxa_names<-,otu_table,character-method	assign-taxa_names
taxa_names<-,phylo,character-method	assign-taxa_names
taxa_names<-,phyloseq,character-method	assign-taxa_names
taxa_names<-,taxonomyTable,character-method	assign-taxa_names
taxa_names<-,XStringSet,character-method	assign-taxa_names
taxa_sums	taxa_sums
taxglom	phyloseq-deprecated
taxonomyTable-class	taxonomyTable-class
taxTab	phyloseq-deprecated
taxtab	phyloseq-deprecated
taxTab<-	phyloseq-deprecated
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	phyloseq-deprecated
tip_glom	tip_glom
topf	topf
topk	topk
topp	topp
transformSampleCounts	transformcounts
transform_sample_counts	transformcounts
tre	phyloseq-deprecated
tre<-	phyloseq-deprecated
tree_layout	tree_layout
UniFrac	UniFrac-methods
UniFrac,phyloseq-method	UniFrac-methods
[,otu_table,ANY,ANY,ANY-method	extract-methods
[,sample_data,ANY,ANY,ANY-method	extract-methods
[,taxonomyTable,ANY,ANY,ANY-method	extract-methods
[,XStringSet,character,ANY,ANY-method	extract-methods