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.
An S4 placeholder of the main phylogenetic tree class from the ape package.
S3 class placeholder definition (list) for phylogenetic trees.
The main experiment-level class for phyloseq data
Depcrecated functions in the phyloseq package.
Handling and analysis of high-throughput phylogenetic sequence data.
Build phyloseq-class objects from their components.
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.