phyloseq: Handling and analysis of high-throughput microbiome census data
Version 1.20.0

phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.

Browse man pages Browse package API and functions Browse package files

AuthorPaul J. McMurdie <joey711@gmail.com>, Susan Holmes <susan@stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain
Bioconductor views Classification Clustering GeneticVariability Metagenomics Microbiome MultipleComparison Sequencing
Date of publicationNone
MaintainerPaul J. McMurdie <joey711@gmail.com>
LicenseAGPL-3
Version1.20.0
URL http://dx.plos.org/10.1371/journal.pone.0061217
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("phyloseq")

Man pages

access: Universal slot accessor function for phyloseq-class.
assign-otu_table: Assign a new OTU Table to 'x'
assign-phy_tree: Assign a (new) phylogenetic tree to 'x'
assign-sample_data: Assign (new) sample_data to 'x'
assign-sample_names: Replace OTU identifier names
assign-taxa_are_rows: Manually change taxa_are_rows through assignment.
assign-taxa_names: Replace OTU identifier names
assign-tax_table: Assign a (new) Taxonomy Table to 'x'
build_tax_table: Build a 'tax_table' from a named possibly-jagged list
capscale-phyloseq-methods: Constrained Analysis of Principal Coordinates, 'capscale'.
cca-rda-phyloseq-methods: Constrained Correspondence Analysis and Redundancy Analysis.
chunkReOrder: Chunk re-order a vector so that specified newstart is first.
data-enterotype: (Data) Enterotypes of the human gut microbiome (2011)
data-esophagus: (Data) Small example dataset from a human esophageal...
data-GlobalPatterns: (Data) Global patterns of 16S rRNA diversity at a depth of...
data-soilrep: (Data) Reproducibility of soil microbiome data (2011)
decorana: S3 class placeholder definition (list) for decorana
distance: Calculate distance, dissimilarity
distanceMethodList: List of distance method keys supported in 'distance'
dist-class: An S4 placeholder for the 'dist' class.
DPCoA: Calculate Double Principle Coordinate Analysis (DPCoA) using...
envHash2otu_table: Convert a sequence-sample hash (like ENV file) into an OTU...
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...
extract-methods: Method extensions to extraction operator for phyloseq...
filterfun_sample: A sample-wise filter function builder analogous to...
filter_taxa: Filter taxa based on across-sample OTU abundance criteria
fix_phylo: Method for fixing problems with phylo-class trees in phyloseq
gapstat_ord: Estimate the gap statistic on an ordination result
genefilter_sample-methods: Filter OTUs with arbitrary function, sample-wise.
get.component.classes: Show the component objects classes and slot names.
get_sample-methods: Returns all abundance values for species 'i'.
getslots.phyloseq: Return the non-empty slot names of a phyloseq object.
get_taxa-methods: Returns all abundance values of sample 'i'.
get_taxa_unique: Get a unique vector of the observed taxa at a particular...
get_variable: Get the values for a particular variable in sample_data
import: Universal import method (wrapper) for phyloseq-package
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...
import_mothur_constaxonomy: Import mothur constaxonomy file and return a taxonomyTable
import_mothur_dist: Import mothur-formatted distance file
import_mothur_groups: Parse mothur group file into a simple hash table.
import_mothur_otulist: Import mothur list file and return as list object in R.
import_mothur_otu_table: Import mothur list and group files and return an otu_table
import_mothur_shared: Import mothur shared file and return an otu_table
import_pyrotagger_tab: Imports a tab-delimited version of the pyrotagger output...
import_qiime: Import function to read the now legacy-format QIIME OTU...
import_qiime_otu_tax: Import now legacy-format QIIME OTU table as a list of two...
import_qiime_sample_data: Import just 'sample_data' file from QIIME pipeline.
import_RDP_cluster: Import RDP cluster file and return otu_table (abundance...
import_RDP_otu: Import new RDP OTU-table format
import_uparse: Import UPARSE file format
import_usearch_uc: Import usearch table format ('.uc') to OTU table
index_reorder: Force index order of phyloseq objects
intersect_taxa: Returns the intersection of species and samples for the...
JSD: Calculate the Jensen-Shannon Divergence (distance)
make_network: Make microbiome network (igraph)
merge_phyloseq: Merge arguments into one phyloseq object.
merge_phyloseq_pair-methods: Merge pair of phyloseq component data objects of the same...
merge_samples-methods: Merge samples based on a sample variable or factor.
merge_taxa-methods: Merge a subset of the species in 'x' into one...
metaMDS: S3 class placeholder definition (list) for metaMDS
microbio_me_qiime: Import microbio.me/qiime (QIIME-DB) data package
mt-methods: Multiple testing of taxa abundance according to sample...
nodeplotblank: Function to avoid plotting node labels
nodeplotboot: Generates a function for labeling bootstrap values on a...
nodeplotdefault: Generates a default node-label function
nsamples-methods: Get the number of samples.
ntaxa-methods: Get the number of taxa/species.
ordinate: Perform an ordination on phyloseq data
otu_table-class: The S4 class for storing taxa-abundance information.
otu_table-methods: Build or access the otu_table.
parseTaxonomy-functions: Parse elements of a taxonomy vector
pcoa: S3 class for ape-calculated MDS results
phylo: S3 class placeholder definition (list) for phylogenetic...
phylo-class: An S4 placeholder of the main phylogenetic tree class from...
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...
phyloseq_to_deseq2: Convert phyloseq data to DESeq2 dds object
phyloseq_to_metagenomeSeq: Convert phyloseq data to MetagenomeSeq MRexperiment object
phy_tree-methods: Retrieve phylogenetic tree ('phylo'-class) from 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...
plot_net: Microbiome Network Plot using ggplot2
plot_network: Microbiome Network Plot using ggplot2
plot_ordination: General ordination plotter based on ggplot2.
plot_phyloseq-methods: 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-methods: Define a subset of samples to keep in a phyloseq object.
prune_taxa-methods: 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...
read_tree: Somewhat flexible tree-import function
read_tree_greengenes: Read GreenGenes tree released in annotated newick format
reconcile_categories: Cleans absent levels in sample_data/data.frame.
refseq-methods: Retrieve reference sequences ('XStringSet'-class) from...
rm_outlierf: Set to FALSE any outlier species greater than f fractional...
sample_data-class: The S4 for storing sample variables.
sample_data-methods: Build or access sample_data.
sample_names-methods: Get sample names.
sample_sums: Returns the total number of individuals observed from each...
sample_variables: Get the sample variables present in sample_data
show-methods: method extensions to show for phyloseq objects.
show_mothur_cutoffs: Show cutoff values available in a mothur file.
splat.phyloseq.objects: Convert 'phyloseq-class' into a named list of its non-empty...
subset_ord_plot: Subset points from an ordination-derived ggplot
subset_samples-methods: Subset samples by sample_data expression
subset_taxa-methods: Subset species by taxonomic expression
taxa_are_rows-methods: Access taxa_are_rows slot from otu_table objects.
taxa_names-methods: Get species / taxa names.
taxa_sums: Returns the total number of individuals observed from each...
tax_glom: Agglomerate taxa of the same type.
taxonomyTable-class: An S4 class that holds taxonomic classification data as a...
tax_table-methods: Build or access the taxonomyTable.
threshrank: Thresholded rank transformation.
threshrankfun: A closure version of the 'threshrank' function.
tip_glom: Agglomerate closely-related taxa using single-linkage...
topf: Make filter fun. that returns the top f fraction of taxa in a...
topk: Make filter fun. the most abundant 'k' taxa
topp: Make filter fun. that returns the most abundant 'p' fraction...
transformcounts: Transform abundance data in an 'otu_table', sample-by-sample.
transpose-methods: Transpose 'otu_table-class' or 'phyloseq-class'
tree_layout: Returns a data table defining the line segments of a...
UniFrac-methods: Calculate weighted or unweighted (Fast) UniFrac distance for...

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
ape_node_depth_edge_length 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

Files

DESCRIPTION
NAMESPACE
R
R/IO-methods.R
R/allClasses.R
R/allData.R
R/allPackage.R
R/almostAllAccessors.R
R/as-methods.R
R/assignment-methods.R
R/deprecated_functions.R
R/distance-methods.R
R/extend_DESeq2.R
R/extend_metagenomeSeq.R
R/extend_vegan.R
R/extract-methods.R
R/merge-methods.R
R/multtest-wrapper.R
R/network-methods.R
R/ordination-methods.R
R/otuTable-class.R
R/phylo-class.R
R/phyloseq-class.R
R/plot-methods.R
R/sampleData-class.R
R/show-methods.R
R/taxonomyTable-class.R
R/transform_filter-methods.R
R/validity-methods.R
README.html
README.md
TODO.txt
build
build/vignette.rds
data
data/GlobalPatterns.RData
data/datalist
data/enterotype.RData
data/esophagus.RData
data/soilrep.RData
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/Unweighted_UniFrac.RData
inst/doc/phyloseq-FAQ.R
inst/doc/phyloseq-FAQ.Rmd
inst/doc/phyloseq-FAQ.html
inst/doc/phyloseq-analysis.R
inst/doc/phyloseq-analysis.Rmd
inst/doc/phyloseq-analysis.html
inst/doc/phyloseq-basics.R
inst/doc/phyloseq-basics.Rmd
inst/doc/phyloseq-basics.html
inst/doc/phyloseq-mixture-models.R
inst/doc/phyloseq-mixture-models.Rmd
inst/doc/phyloseq-mixture-models.html
inst/extdata
inst/extdata/GP_otu_table_rand_short.txt.gz
inst/extdata/GP_tree_rand_short.newick.gz
inst/extdata/biom-refseq.fasta
inst/extdata/biom-tree.phy
inst/extdata/esophagus.fn.list.gz
inst/extdata/esophagus.fn.shared.gz
inst/extdata/esophagus.good.groups.gz
inst/extdata/esophagus.tree.gz
inst/extdata/gg13-5-73.tree.gz
inst/extdata/gp500-pycogent.py
inst/extdata/gp500-uuf.csv
inst/extdata/gp500-wuf.csv
inst/extdata/gp500-wufu.csv
inst/extdata/gp500test.env.txt
inst/extdata/gp500test.tree
inst/extdata/master_map.txt
inst/extdata/min_dense_otu_table.biom
inst/extdata/min_sparse_otu_table.biom
inst/extdata/mothur_example.cons.taxonomy.gz
inst/extdata/qiime500-refseq.fasta
inst/extdata/rformat_dist_0.03.txt.gz
inst/extdata/rich_dense_otu_table.biom
inst/extdata/rich_sparse_otu_table.biom
inst/extdata/study_1457_split_library_seqs_and_mapping.zip
inst/extdata/study_816_split_library_seqs_and_mapping.tar.gz
inst/extdata/study_816_split_library_seqs_and_mapping.zip
inst/extdata/study_gp.txt
inst/extdata/usearch.uc
inst/scripts
inst/scripts/installer.R
man
man/DPCoA.Rd
man/JSD.Rd
man/UniFrac-methods.Rd
man/access.Rd
man/assign-otu_table.Rd
man/assign-phy_tree.Rd
man/assign-sample_data.Rd
man/assign-sample_names.Rd
man/assign-tax_table.Rd
man/assign-taxa_are_rows.Rd
man/assign-taxa_names.Rd
man/build_tax_table.Rd
man/capscale-phyloseq-methods.Rd
man/cca-rda-phyloseq-methods.Rd
man/chunkReOrder.Rd
man/data-GlobalPatterns.Rd
man/data-enterotype.Rd
man/data-esophagus.Rd
man/data-soilrep.Rd
man/decorana.Rd
man/dist-class.Rd
man/distance.Rd
man/distanceMethodList.Rd
man/envHash2otu_table.Rd
man/estimate_richness.Rd
man/export_env_file.Rd
man/export_mothur_dist.Rd
man/extract-methods.Rd
man/filter_taxa.Rd
man/filterfun_sample.Rd
man/fix_phylo.Rd
man/gapstat_ord.Rd
man/genefilter_sample-methods.Rd
man/get.component.classes.Rd
man/get_sample-methods.Rd
man/get_taxa-methods.Rd
man/get_taxa_unique.Rd
man/get_variable.Rd
man/getslots.phyloseq.Rd
man/import.Rd
man/import_RDP_cluster.Rd
man/import_RDP_otu.Rd
man/import_biom.Rd
man/import_env_file.Rd
man/import_mothur.Rd
man/import_mothur_constaxonomy.Rd
man/import_mothur_dist.Rd
man/import_mothur_groups.Rd
man/import_mothur_otu_table.Rd
man/import_mothur_otulist.Rd
man/import_mothur_shared.Rd
man/import_pyrotagger_tab.Rd
man/import_qiime.Rd
man/import_qiime_otu_tax.Rd
man/import_qiime_sample_data.Rd
man/import_uparse.Rd
man/import_usearch_uc.Rd
man/index_reorder.Rd
man/intersect_taxa.Rd
man/make_network.Rd
man/merge_phyloseq.Rd
man/merge_phyloseq_pair-methods.Rd
man/merge_samples-methods.Rd
man/merge_taxa-methods.Rd
man/metaMDS.Rd
man/microbio_me_qiime.Rd
man/mt-methods.Rd
man/nodeplotblank.Rd
man/nodeplotboot.Rd
man/nodeplotdefault.Rd
man/nsamples-methods.Rd
man/ntaxa-methods.Rd
man/ordinate.Rd
man/otu_table-class.Rd
man/otu_table-methods.Rd
man/parseTaxonomy-functions.Rd
man/pcoa.Rd
man/phy_tree-methods.Rd
man/phylo-class.Rd
man/phylo.Rd
man/phyloseq-class.Rd
man/phyloseq-deprecated.Rd
man/phyloseq-package.Rd
man/phyloseq.Rd
man/phyloseq_to_deseq2.Rd
man/phyloseq_to_metagenomeSeq.Rd
man/plot_bar.Rd
man/plot_clusgap.Rd
man/plot_heatmap.Rd
man/plot_net.Rd
man/plot_network.Rd
man/plot_ordination.Rd
man/plot_phyloseq-methods.Rd
man/plot_richness.Rd
man/plot_scree.Rd
man/plot_tree.Rd
man/prune_samples-methods.Rd
man/prune_taxa-methods.Rd
man/psmelt.Rd
man/rank_names.Rd
man/rarefy_even_depth.Rd
man/read_tree.Rd
man/read_tree_greengenes.Rd
man/reconcile_categories.Rd
man/refseq-methods.Rd
man/rm_outlierf.Rd
man/sample_data-class.Rd
man/sample_data-methods.Rd
man/sample_names-methods.Rd
man/sample_sums.Rd
man/sample_variables.Rd
man/show-methods.Rd
man/show_mothur_cutoffs.Rd
man/splat.phyloseq.objects.Rd
man/subset_ord_plot.Rd
man/subset_samples-methods.Rd
man/subset_taxa-methods.Rd
man/tax_glom.Rd
man/tax_table-methods.Rd
man/taxa_are_rows-methods.Rd
man/taxa_names-methods.Rd
man/taxa_sums.Rd
man/taxonomyTable-class.Rd
man/threshrank.Rd
man/threshrankfun.Rd
man/tip_glom.Rd
man/topf.Rd
man/topk.Rd
man/topp.Rd
man/transformcounts.Rd
man/transpose-methods.Rd
man/tree_layout.Rd
tests
tests/testthat
tests/testthat-phyloseq.R
tests/testthat/test-IO.R
tests/testthat/test-distance.R
tests/testthat/test-merge.R
tests/testthat/test-phyloseq.R
tests/testthat/test-plot.R
tests/testthat/test-rarefy.R
tests/testthat/test-subset.R
tests/testthat/test-transform.R
vignettes
vignettes/import_qiime_directory_structure.jpg
vignettes/phyloseq-FAQ.Rmd
vignettes/phyloseq-analysis.Rmd
vignettes/phyloseq-basics.Rmd
vignettes/phyloseq-mixture-models.Rmd
vignettes/phyloseq_classes_7.png
phyloseq documentation built on May 20, 2017, 10:01 p.m.