phyloseq

Calculate Double Principle Coordinate Analysis (DPCoA) using phylogenetic distance

Calculate the Jensen-Shannon Divergence (distance)

Calculate weighted or unweighted (Fast) UniFrac distance for all sample pairs.

Universal slot accessor function for phyloseq-class.

Assign a new OTU Table to x

Assign a (new) phylogenetic tree to x

Assign (new) sample_data to x

Replace OTU identifier names

Assign a (new) Taxonomy Table to x

Manually change taxa_are_rows through assignment.

Replace OTU identifier names

Build a tax_table from a named possibly-jagged list

Constrained Analysis of Principal Coordinates, capscale.

Constrained Correspondence Analysis and Redundancy Analysis.

Chunk re-order a vector so that specified newstart is first.

(Data) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2011)

(Data) Enterotypes of the human gut microbiome (2011)

(Data) Small example dataset from a human esophageal community (2004)

(Data) Reproducibility of soil microbiome data (2011)

S3 class placeholder definition (list) for decorana

An S4 placeholder for the dist class.

Calculate distance, dissimilarity

List of distance method keys supported in distance

Convert a sequence-sample hash (like ENV file) into an OTU table.

Summarize alpha diversity

Export environment (ENV) file for UniFrac Server.

Export a distance object as .names and .dist files for mothur

Method extensions to extraction operator for phyloseq objects.

Filter taxa based on across-sample OTU abundance criteria

A sample-wise filter function builder analogous to filterfun.

Method for fixing problems with phylo-class trees in phyloseq

Estimate the gap statistic on an ordination result

Filter OTUs with arbitrary function, sample-wise.

Show the component objects classes and slot names.

Returns all abundance values for species i.

Returns all abundance values of sample i.

Get a unique vector of the observed taxa at a particular taxonomic rank

Get the values for a particular variable in sample_data

Return the non-empty slot names of a phyloseq object.

Universal import method (wrapper) for phyloseq-package

Import RDP cluster file and return otu_table (abundance table).

Import new RDP OTU-table format

Import phyloseq data from biom-format file

Read a UniFrac-formatted ENV file.

General function for importing mothur data files into phyloseq.

Import mothur constaxonomy file and return a taxonomyTable

Import mothur-formatted distance file

Parse mothur group file into a simple hash table.

Import mothur list and group files and return an otu_table

Import mothur list file and return as list object in R.

Import mothur shared file and return an otu_table

Imports a tab-delimited version of the pyrotagger output file.

Import function to read the now legacy-format QIIME OTU table.

Import now legacy-format QIIME OTU table as a list of two matrices.

Import just sample_data file from QIIME pipeline.

Import UPARSE file format

Import usearch table format (.uc) to OTU table

Force index order of phyloseq objects

Returns the intersection of species and samples for the components of x

Make microbiome network (igraph)

Merge arguments into one phyloseq object.

Merge pair of phyloseq component data objects of the same class.

Merge samples based on a sample variable or factor.

Merge a subset of the species in x into one species/taxa/OTU.

S3 class placeholder definition (list) for metaMDS

Import microbio.me/qiime (QIIME-DB) data package

Multiple testing of taxa abundance according to sample categories/classes

Function to avoid plotting node labels

Generates a function for labeling bootstrap values on a phylogenetic tree.

Generates a default node-label function

Get the number of samples.

Get the number of taxa/species.

Perform an ordination on phyloseq data

The S4 class for storing taxa-abundance information.

Build or access the otu_table.

Parse elements of a taxonomy vector

S3 class for ape-calculated MDS results

Retrieve phylogenetic tree (phylo-class) from object.

S3 class placeholder definition (list) for phylogenetic trees.

An S4 placeholder of the main phylogenetic tree class from the ape package.

Build phyloseq-class objects from their components.

The main experiment-level class for phyloseq data

Depcrecated functions in the phyloseq package.

Handling and analysis of high-throughput phylogenetic sequence data.

Convert phyloseq data to DESeq2 dds object

Convert phyloseq data to MetagenomeSeq MRexperiment object

A flexible, informative barplot phyloseq data

Create a ggplot summary of gap statistic results

Create an ecologically-organized heatmap using ggplot2 graphics

Microbiome Network Plot using ggplot2

Microbiome Network Plot using ggplot2

General ordination plotter based on ggplot2.

Generic plot defaults for phyloseq.

Plot alpha diversity, flexibly with ggplot2

General ordination eigenvalue plotter using ggplot2.

Plot a phylogenetic tree with optional annotations

Define a subset of samples to keep in a phyloseq object.

Prune unwanted OTUs / taxa from a phylogenetic object.

Melt phyloseq data object into large data.frame

Retrieve the names of the taxonomic ranks

Resample an OTU table such that all samples have the same library size.

Somewhat flexible tree-import function

Read GreenGenes tree released in annotated newick format

Cleans absent levels in sample_data/data.frame.

Retrieve reference sequences (XStringSet-class) from object.

Set to FALSE any outlier species greater than f fractional abundance.

The S4 for storing sample variables.

Build or access sample_data.

Get sample names.

Returns the total number of individuals observed from each sample.

Get the sample variables present in sample_data

method extensions to show for phyloseq objects.

Show cutoff values available in a mothur file.

Convert phyloseq-class into a named list of its non-empty components.

Subset points from an ordination-derived ggplot

Subset samples by sample_data expression

Subset species by taxonomic expression

Agglomerate taxa of the same type.

Build or access the taxonomyTable.

Access taxa_are_rows slot from otu_table objects.

Get species / taxa names.

Returns the total number of individuals observed from each species/taxa/OTU.

An S4 class that holds taxonomic classification data as a character matrix.

Thresholded rank transformation.

A closure version of the threshrank function.

Agglomerate closely-related taxa using single-linkage clustering.

Make filter fun. that returns the top f fraction of taxa in a sample.

Make filter fun. the most abundant k taxa

Make filter fun. that returns the most abundant p fraction of taxa

Transform abundance data in an otu_table, sample-by-sample.

Transpose otu_table-class or phyloseq-class

Returns a data table defining the line segments of a phylogenetic tree.