DPCoA                   Calculate Double Principle Coordinate Analysis
                        (DPCoA) using phylogenetic distance
UniFrac                 Calculate weighted or unweighted (Fast) UniFrac
                        distance for all sample pairs.
[,otu_table,ANY,ANY,ANY-method
                        Method extensions to extraction operator for
                        phyloseq objects.
access                  Universal slot accessor function for
                        phyloseq-class.
build_tax_table         Build a 'tax_table' from a named
                        possibly-jagged list
data-GlobalPatterns     (Data) Global patterns of 16S rRNA diversity at
                        a depth of millions of sequences per sample
                        (2011)
data-enterotype         (Data) Enterotypes of the human gut microbiome
                        (2011)
data-esophagus          (Data) Small example dataset from a human
                        esophageal community (2004)
data-soilrep            (Data) Reproducibility of soil microbiome data
                        (2011)
dist-class              An S4 placeholder for the 'dist' class.
distance                Calculate distance, dissimilarity
distanceMethodList      List of distance method keys supported in
                        'distance'
estimate_richness       Summarize alpha diversity
export_env_file         Export environment (ENV) file for UniFrac
                        Server.
export_mothur_dist      Export a distance object as '.names' and
                        '.dist' files for mothur
filter_taxa             Filter taxa based on across-sample OTU
                        abundance criteria
filterfun_sample        A sample-wise filter function builder analogous
                        to 'filterfun'.
gapstat_ord             Estimate the gap statistic on an ordination
                        result
genefilter_sample       Filter OTUs with arbitrary function,
                        sample-wise.
get_sample              Returns all abundance values for species 'i'.
get_taxa                Returns all abundance values of sample 'i'.
get_taxa_unique         Get a unique vector of the observed taxa at a
                        particular taxonomic rank
get_variable            Get the values for a particular variable in
                        sample_data
getslots.phyloseq       Return the non-empty slot names of a phyloseq
                        object.
import                  Universal import method (wrapper) for
                        phyloseq-package
import_RDP_cluster      Import RDP cluster file and return otu_table
                        (abundance table).
import_RDP_otu          Import new RDP OTU-table format
import_biom             Import phyloseq data from biom-format file
import_env_file         Read a UniFrac-formatted ENV file.
import_mothur           General function for importing mothur data
                        files into phyloseq.
import_mothur_dist      Import mothur-formatted distance file
import_pyrotagger_tab   Imports a tab-delimited version of the
                        pyrotagger output file.
import_qiime            Import function to read the now legacy-format
                        QIIME OTU table.
import_qiime_otu_tax    Import now legacy-format QIIME OTU table as a
                        list of two matrices.
import_qiime_sample_data
                        Import just 'sample_data' file from QIIME
                        pipeline.
import_uparse           Import UPARSE file format
import_usearch_uc       Import usearch table format ('.uc') to OTU
                        table
make_network            Make microbiome network (igraph)
merge_phyloseq          Merge arguments into one phyloseq object.
merge_phyloseq_pair     Merge pair of phyloseq component data objects
                        of the same class.
merge_samples           Merge samples based on a sample variable or
                        factor.
merge_taxa              Merge a subset of the species in 'x' into one
                        species/taxa/OTU.
microbio_me_qiime       Import microbio.me/qiime (QIIME-DB) data
                        package
mt                      Multiple testing of taxa abundance according to
                        sample categories/classes
nodeplotblank           Function to avoid plotting node labels
nodeplotboot            Generates a function for labeling bootstrap
                        values on a phylogenetic tree.
nodeplotdefault         Generates a default node-label function
nsamples                Get the number of samples.
ntaxa                   Get the number of taxa/species.
ordinate                Perform an ordination on phyloseq data
otu_table               Build or access the otu_table.
otu_table-class         The S4 class for storing taxa-abundance
                        information.
otu_table<-             Assign a new OTU Table to 'x'
parse_taxonomy_default
                        Parse elements of a taxonomy vector
phy_tree                Retrieve phylogenetic tree ('phylo'-class) from
                        object.
phy_tree<-              Assign a (new) phylogenetic tree to 'x'
phylo-class             An S4 placeholder of the main phylogenetic tree
                        class from the ape package.
phyloseq                Build phyloseq-class objects from their
                        components.
phyloseq-class          The main experiment-level class for phyloseq
                        data
phyloseq-deprecated     Depcrecated functions in the phyloseq package.
phyloseq-package        Handling and analysis of high-throughput
                        phylogenetic sequence data.
phyloseq_to_deseq2      Convert phyloseq data to DESeq2 dds object
phyloseq_to_metagenomeSeq
                        Convert phyloseq data to MetagenomeSeq
                        MRexperiment object
plot_bar                A flexible, informative barplot phyloseq data
plot_clusgap            Create a ggplot summary of gap statistic
                        results
plot_heatmap            Create an ecologically-organized heatmap using
                        ggplot2 graphics
plot_net                Microbiome Network Plot using ggplot2
plot_network            Microbiome Network Plot using ggplot2
plot_ordination         General ordination plotter based on ggplot2.
plot_phyloseq           Generic plot defaults for phyloseq.
plot_richness           Plot alpha diversity, flexibly with ggplot2
plot_scree              General ordination eigenvalue plotter using
                        ggplot2.
plot_tree               Plot a phylogenetic tree with optional
                        annotations
prune_samples           Define a subset of samples to keep in a
                        phyloseq object.
prune_taxa              Prune unwanted OTUs / taxa from a phylogenetic
                        object.
psmelt                  Melt phyloseq data object into large data.frame
rank_names              Retrieve the names of the taxonomic ranks
rarefy_even_depth       Resample an OTU table such that all samples
                        have the same library size.
read_tree               Somewhat flexible tree-import function
read_tree_greengenes    Read GreenGenes tree released in annotated
                        newick format
refseq                  Retrieve reference sequences
                        ('XStringSet'-class) from object.
rm_outlierf             Set to FALSE any outlier species greater than f
                        fractional abundance.
sample_data             Build or access sample_data.
sample_data-class       The S4 for storing sample variables.
sample_data<-           Assign (new) sample_data to 'x'
sample_names            Get sample names.
sample_names<-          Replace OTU identifier names
sample_sums             Returns the total number of individuals
                        observed from each sample.
sample_variables        Get the sample variables present in sample_data
show,otu_table-method   method extensions to show for phyloseq objects.
show_mothur_cutoffs     Show cutoff values available in a mothur file.
subset_ord_plot         Subset points from an ordination-derived ggplot
subset_samples          Subset samples by sample_data expression
subset_taxa             Subset species by taxonomic expression
t                       Transpose 'otu_table-class' or 'phyloseq-class'
tax_glom                Agglomerate taxa of the same type.
tax_table               Build or access the taxonomyTable.
tax_table<-             Assign a (new) Taxonomy Table to 'x'
taxa_are_rows           Access taxa_are_rows slot from otu_table
                        objects.
taxa_are_rows<-         Manually change taxa_are_rows through
                        assignment.
taxa_names              Get species / taxa names.
taxa_names<-            Replace OTU identifier names
taxa_sums               Returns the total number of individuals
                        observed from each species/taxa/OTU.
taxonomyTable-class     An S4 class that holds taxonomic classification
                        data as a character matrix.
threshrank              Thresholded rank transformation.
threshrankfun           A closure version of the 'threshrank' function.
tip_glom                Agglomerate closely-related taxa using
                        single-linkage clustering.
topf                    Make filter fun. that returns the top f
                        fraction of taxa in a sample.
topk                    Make filter fun. the most abundant 'k' taxa
topp                    Make filter fun. that returns the most abundant
                        'p' fraction of taxa
transform_sample_counts
                        Transform abundance data in an 'otu_table',
                        sample-by-sample.
tree_layout             Returns a data table defining the line segments
                        of a phylogenetic tree.
