/usr/lib/R/site-library/phyloseq/help/AnIndex is in r-bioc-phyloseq 1.22.3-1.
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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
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