API for phyloseq
Handling and analysis of high-throughput microbiome census data

Global functions
DPCoA Man page Source code
GlobalPatterns Man page
JSD Man page
RadialTheta Source code
UniFrac Man page
UniFrac,phyloseq-method Man page
[,XStringSet,character,ANY,ANY-method Man page
[,otu_table,ANY,ANY,ANY-method Man page
[,sample_data,ANY,ANY,ANY-method Man page
[,taxonomyTable,ANY,ANY,ANY-method Man page
access Man page Source code
assign-otu_table Man page
assign-phy_tree Man page
assign-sample_data Man page
assign-sample_names Man page
assign-tax_table Man page
assign-taxa_are_rows Man page
assign-taxa_names Man page
build_tax_table Man page Source code
capscale.phyloseq Man page
capscale.phyloseq,phyloseq,formula,character-method Man page
capscale.phyloseq,phyloseq,formula,dist-method Man page
cca.phyloseq Man page
cca.phyloseq,otu_table,ANY-method Man page
cca.phyloseq,otu_table-method Man page
cca.phyloseq,phyloseq,NULL-method Man page
cca.phyloseq,phyloseq,formula-method Man page
chunkReOrder Man page Source code
data-GlobalPatterns Man page
data-enterotype Man page
data-esophagus Man page
data-soilrep Man page
decorana Man page
deprecated_phyloseq_function Man page Source code
dist-class Man page
distance Man page
distance,otu_table,character-method Man page
distance,phyloseq,ANY-method Man page
distance,phyloseq,character-method Man page
distanceMethodList Man page
enterotype Man page
envHash2otu_table Man page Source code
esophagus Man page
estimate_richness Man page Source code
export_env_file Man page Source code
export_mothur_dist Man page Source code
extract_eigenvalue Source code
extract_eigenvalue.cca Source code
extract_eigenvalue.decorana Source code
extract_eigenvalue.default Source code
extract_eigenvalue.dpcoa Source code
extract_eigenvalue.pcoa Source code
extract_eigenvalue.rda Source code
f_comp_ps Source code
fastUniFrac Source code
filter_taxa Man page Source code
filterfunSample Man page Source code
filterfun_sample Man page Source code
fix_phylo Man page
fix_phylo,phylo-method Man page
gapstat_ord Man page Source code
genefilterSample Man page Source code
genefilter_sample Man page
genefilter_sample,matrix-method Man page
genefilter_sample,otu_table-method Man page
genefilter_sample,phyloseq-method Man page
get.component.classes Man page Source code
getSamples Man page Source code
getSpecies Man page Source code
getTaxa Man page Source code
getVariable Man page Source code
get_dpcoa_sites_coords Source code
get_dpcoa_species_coords Source code
get_sample Man page
get_sample,otu_table-method Man page
get_sample,phyloseq-method Man page
get_taxa Man page
get_taxa,otu_table-method Man page
get_taxa,phyloseq-method Man page
get_taxa_unique Man page Source code
get_variable Man page Source code
getslots.phyloseq Man page Source code
howtolabnodes Source code
import Man page Source code
import_RDP_cluster Man page Source code
import_RDP_otu Man page Source code
import_biom Man page Source code
import_env_file Man page Source code
import_mothur Man page Source code
import_mothur_constaxonomy Man page Source code
import_mothur_dist Man page Source code
import_mothur_groups Man page Source code
import_mothur_otu_table Man page Source code
import_mothur_otulist Man page Source code
import_mothur_shared Man page Source code
import_pyrotagger_tab Man page Source code
import_qiime Man page Source code
import_qiime_otu_tax Man page Source code
import_qiime_sampleData Man page Source code
import_qiime_sample_data Man page Source code
import_uparse Man page Source code
import_usearch_uc Man page Source code
index_reorder Man page
index_reorder,phyloseq-method Man page
intersect_samples Source code
intersect_taxa Man page Source code
is.component.class Source code
make_network Man page Source code
manytextsize Source code
merge_phyloseq Man page Source code
merge_phyloseq_pair Man page
merge_phyloseq_pair,XStringSet,XStringSet-method Man page
merge_phyloseq_pair,otu_table,otu_table-method Man page
merge_phyloseq_pair,phylo,phylo-method Man page
merge_phyloseq_pair,sample_data,sample_data-method Man page
merge_phyloseq_pair,taxonomyTable,taxonomyTable-method Man page
merge_samples Man page
merge_samples,otu_table-method Man page
merge_samples,phyloseq-method Man page
merge_samples,sample_data-method Man page
merge_species Man page Source code
merge_taxa Man page
merge_taxa,XStringSet-method Man page
merge_taxa,otu_table-method Man page
merge_taxa,phylo-method Man page
merge_taxa,phyloseq-method Man page
merge_taxa,sample_data-method Man page
merge_taxa,taxonomyTable-method Man page
merge_taxa.indices.internal Source code
metaMDS Man page
microbio_me_qiime Man page Source code
mt Man page
mt,otu_table,character-method Man page
mt,otu_table,factor-method Man page
mt,otu_table,integer-method Man page
mt,otu_table,logical-method Man page
mt,otu_table,numeric-method Man page
mt,phyloseq,ANY-method Man page
mt.phyloseq.internal Source code
nodeplotblank Man page Source code
nodeplotboot Man page Source code
nodeplotdefault Man page Source code
nodesnotlabeled Source code
nsamples Man page
nsamples,ANY-method Man page
nsamples,otu_table-method Man page
nsamples,phyloseq-method Man page
nsamples,sample_data-method Man page
nspecies Man page Source code
ntaxa Man page
ntaxa,ANY-method Man page
ntaxa,XStringSet-method Man page
ntaxa,otu_table-method Man page
ntaxa,phylo-method Man page
ntaxa,phyloseq-method Man page
ntaxa,taxonomyTable-method Man page
ordinate Man page Source code
originalUniFrac Source code
otuTable Man page Source code
otuTable<- Man page
otu_table Man page
otu_table,ANY-method Man page
otu_table,data.frame-method Man page
otu_table,matrix-method Man page
otu_table,otu_table-method Man page
otu_table,phyloseq-method Man page
otu_table-class Man page
otu_table<- Man page
otu_table<-,otu_table,otu_table-method Man page
otu_table<-,phyloseq,otu_table-method Man page
otu_table<-,phyloseq,phyloseq-method Man page
parse_taxonomy_default Man page Man page Man page Source code
parse_taxonomy_greengenes Man page Source code
parse_taxonomy_qiime Man page Source code
pcoa Man page
phy_tree Man page
phy_tree,ANY-method Man page
phy_tree,phylo-method Man page
phy_tree<- Man page
phy_tree<-,phyloseq,phylo-method Man page
phy_tree<-,phyloseq,phyloseq-method Man page
phylo Man page
phylo-class Man page
phyloseq Man page Source code
phyloseq-class Man page
phyloseq-deprecated Man page
phyloseq-deprecated-package Man page
phyloseq-package Man page
phyloseq_JSD_pair Source code
phyloseq_to_deseq2 Man page Source code
phyloseq_to_metagenomeSeq Man page Source code
plot_bar Man page Source code
plot_clusgap Man page Source code
plot_heatmap Man page Source code
plot_net Man page Source code
plot_network Man page Source code
plot_ordination Man page Source code
plot_phyloseq Man page
plot_phyloseq,phyloseq-method Man page
plot_richness Man page Source code
plot_richness_estimates Man page Source code
plot_scree Man page Source code
plot_taxa_bar Man page Source code
plot_tree Man page Source code
prune_samples Man page
prune_samples,character,otu_table-method Man page
prune_samples,character,phyloseq-method Man page
prune_samples,character,sample_data-method Man page
prune_samples,logical,ANY-method Man page
prune_species Man page Source code
prune_taxa Man page
prune_taxa,NULL,ANY-method Man page
prune_taxa,character,XStringSet-method Man page
prune_taxa,character,otu_table-method Man page
prune_taxa,character,phylo-method Man page
prune_taxa,character,phyloseq-method Man page
prune_taxa,character,sample_data-method Man page
prune_taxa,character,taxonomyTable-method Man page
prune_taxa,logical,ANY-method Man page
psmelt Man page Source code
rank.names Man page Source code
rank_names Man page Source code
rarefaction_subsample Source code
rarefy_even_depth Man page Source code
rda.phyloseq Man page
read_tree Man page Source code
read_tree_greengenes Man page Source code
reconcile_categories Man page Source code
refseq Man page
refseq,ANY-method Man page
refseq,XStringSet-method Man page
rm.na.phyloseq Source code
rm_outlierf Man page Source code
rp.joint.fill Source code
samData Man page Source code
sam_data Man page Source code
sam_data<- Man page
sample.components Source code
sample.names Man page Source code
sample.variables Man page Source code
sampleData Man page Source code
sampleData<- Man page
sampleNames Man page Source code
sampleSums Man page Source code
sample_data Man page
sample_data,ANY-method Man page
sample_data,data.frame-method Man page
sample_data-class Man page
sample_data<- Man page
sample_names Man page
sample_names,ANY-method Man page
sample_names,otu_table-method Man page
sample_names,phyloseq-method Man page
sample_names,sample_data-method Man page
sample_names<- Man page
sample_names<-,ANY,ANY-method Man page
sample_names<-,ANY,character-method Man page
sample_names<-,otu_table,character-method Man page
sample_names<-,phyloseq,character-method Man page
sample_names<-,sample_data,character-method Man page
sample_sums Man page Source code
sample_variables Man page Source code
scores.dpcoa Source code
scores.pcoa Source code
select_mothur_cutoff Source code
show,otu_table-method Man page
show,phyloseq-method Man page
show,sample_data-method Man page
show,taxonomyTable-method Man page
show_mothur_cutoffs Man page Source code
show_mothur_list_cutoffs Man page Source code
soilrep Man page
species.names Man page Source code
speciesAreRows Man page Source code
speciesAreRows<- Man page
speciesSums Man page Source code
speciesarerows Man page Source code
splat.phyloseq.objects Man page Source code
subset_ord_plot Man page Source code
subset_samples Man page Source code
subset_species Man page Source code
subset_taxa Man page Source code
t Man page
t,otu_table-method Man page
t,phyloseq-method Man page
taxTab Man page Source code
taxTab<- Man page
tax_glom Man page Source code
tax_table Man page
tax_table,ANY-method Man page
tax_table,data.frame-method Man page
tax_table,matrix-method Man page
tax_table<- Man page
tax_table<-,phyloseq,ANY-method Man page
tax_table<-,phyloseq,taxonomyTable-method Man page
tax_table<-,taxonomyTable,ANY-method Man page
tax_table<-,taxonomyTable,taxonomyTable-method Man page
taxa.components Source code
taxa_are_rows Man page
taxa_are_rows,ANY-method Man page
taxa_are_rows,otu_table-method Man page
taxa_are_rows,phyloseq-method Man page
taxa_are_rows<- Man page
taxa_are_rows<-,otu_table,logical-method Man page
taxa_are_rows<-,phyloseq,logical-method Man page
taxa_names Man page
taxa_names,ANY-method Man page
taxa_names,XStringSet-method Man page
taxa_names,otu_table-method Man page
taxa_names,phylo-method Man page
taxa_names,phyloseq-method Man page
taxa_names,sample_data-method Man page
taxa_names,taxonomyTable-method Man page
taxa_names<- Man page
taxa_names<-,ANY,ANY-method Man page
taxa_names<-,ANY,character-method Man page
taxa_names<-,XStringSet,character-method Man page
taxa_names<-,otu_table,character-method Man page
taxa_names<-,phylo,character-method Man page
taxa_names<-,phyloseq,character-method Man page
taxa_names<-,taxonomyTable,character-method Man page
taxa_sums Man page Source code
taxaplot Man page Source code
taxglom Man page Source code
taxonomyTable-class Man page
taxtab Man page Source code
threshrank Man page Source code
threshrankfun Man page Source code
tip_glom Man page Source code
tipglom Man page Source code
topf Man page Source code
topk Man page Source code
topp Man page Source code
transformSampleCounts Man page Man page
transform_sample_counts Man page Source code
tre Man page Source code
tre<- Man page
tree_layout Man page Source code
validTaxonomyTable Source code
validotu_table Source code
validphyloseq Source code
validsample_data Source code
veganifyOTU Source code
phyloseq documentation built on July 16, 2018, 6 p.m.