phyloseq
Handling and analysis of high-throughput microbiome census data

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457
Source code
40
Man pages
132
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phyloseq: Handling and analysis of high-throughput microbiome census data
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API

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 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
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 Nov. 8, 2020, 6:41 p.m.

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