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.