A B D E F G I M N O P R S T U misc
| phyloseq-deprecated-package | Depcrecated functions in the phyloseq package. |
| phyloseq-package | Handling and analysis of high-throughput phylogenetic sequence data. |
| 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 |
| data-enterotype | (Data) Enterotypes of the human gut microbiome (2011) |
| data-esophagus | (Data) Small example dataset from a human esophageal community (2004) |
| data-GlobalPatterns | (Data) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2011) |
| data-soilrep | (Data) Reproducibility of soil microbiome data (2011) |
| deprecated_phyloseq_function | Depcrecated functions in the phyloseq package. |
| dist-class | An S4 placeholder for the 'dist' class. |
| distance | Calculate distance, dissimilarity |
| distance-method | Calculate distance, dissimilarity |
| distanceMethodList | List of distance method keys supported in 'distance' |
| DPCoA | Calculate Double Principle Coordinate Analysis (DPCoA) using phylogenetic distance |
| enterotype | (Data) Enterotypes of the human gut microbiome (2011) |
| esophagus | (Data) Small example dataset from a human esophageal community (2004) |
| 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 |
| filterfunSample | Depcrecated functions in the phyloseq package. |
| filterfun_sample | A sample-wise filter function builder analogous to 'filterfun'. |
| filter_taxa | Filter taxa based on across-sample OTU abundance criteria |
| gapstat_ord | Estimate the gap statistic on an ordination result |
| genefilterSample | Depcrecated functions in the phyloseq package. |
| genefilter_sample | Filter OTUs with arbitrary function, sample-wise. |
| genefilter_sample-method | Filter OTUs with arbitrary function, sample-wise. |
| getSamples | Depcrecated functions in the phyloseq package. |
| getslots.phyloseq | Return the non-empty slot names of a phyloseq object. |
| getSpecies | Depcrecated functions in the phyloseq package. |
| getTaxa | Depcrecated functions in the phyloseq package. |
| getVariable | Depcrecated functions in the phyloseq package. |
| get_sample | Returns all abundance values for species 'i'. |
| get_sample-method | Returns all abundance values for species 'i'. |
| get_taxa | Returns all abundance values of sample 'i'. |
| get_taxa-method | 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 |
| GlobalPatterns | (Data) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2011) |
| 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 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_sampleData | Depcrecated functions in the phyloseq package. |
| import_qiime_sample_data | Import just 'sample_data' file from QIIME pipeline. |
| import_RDP_cluster | Import RDP cluster file and return otu_table (abundance table). |
| 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 |
| 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_phyloseq_pair-method | Merge pair of phyloseq component data objects of the same class. |
| merge_samples | Merge samples based on a sample variable or factor. |
| merge_samples-method | Merge samples based on a sample variable or factor. |
| merge_species | Depcrecated functions in the phyloseq package. |
| merge_taxa | Merge a subset of the species in 'x' into one species/taxa/OTU. |
| merge_taxa-method | 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 |
| mt-method | 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. |
| nsamples-method | Get the number of samples. |
| nspecies | Depcrecated functions in the phyloseq package. |
| ntaxa | Get the number of taxa/species. |
| ntaxa-method | Get the number of taxa/species. |
| ordinate | Perform an ordination on phyloseq data |
| otuTable | Depcrecated functions in the phyloseq package. |
| otuTable<- | Depcrecated functions in the phyloseq package. |
| otu_table | Build or access the otu_table. |
| otu_table-class | The S4 class for storing taxa-abundance information. |
| otu_table-method | Build or access the otu_table. |
| otu_table<- | Assign a new OTU Table to 'x' |
| otu_table<--method | Assign a new OTU Table to 'x' |
| parse_taxonomy_default | Parse elements of a taxonomy vector |
| parse_taxonomy_greengenes | Parse elements of a taxonomy vector |
| parse_taxonomy_qiime | Parse elements of a taxonomy vector |
| 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_to_deseq2 | Convert phyloseq data to DESeq2 dds object |
| phyloseq_to_metagenomeSeq | Convert phyloseq data to MetagenomeSeq MRexperiment object |
| phy_tree | Retrieve phylogenetic tree ('phylo'-class) from object. |
| phy_tree-method | Retrieve phylogenetic tree ('phylo'-class) from object. |
| phy_tree<- | Assign a (new) phylogenetic tree to 'x' |
| phy_tree<--method | Assign a (new) phylogenetic tree to 'x' |
| 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_phyloseq-method | Generic plot defaults for phyloseq. |
| plot_richness | Plot alpha diversity, flexibly with ggplot2 |
| plot_richness_estimates | Depcrecated functions in the phyloseq package. |
| plot_scree | General ordination eigenvalue plotter using ggplot2. |
| plot_taxa_bar | Depcrecated functions in the phyloseq package. |
| plot_tree | Plot a phylogenetic tree with optional annotations |
| prune_samples | Define a subset of samples to keep in a phyloseq object. |
| prune_samples-method | Define a subset of samples to keep in a phyloseq object. |
| prune_species | Depcrecated functions in the phyloseq package. |
| prune_taxa | Prune unwanted OTUs / taxa from a phylogenetic object. |
| prune_taxa-method | Prune unwanted OTUs / taxa from a phylogenetic object. |
| psmelt | Melt phyloseq data object into large data.frame |
| rank.names | Depcrecated functions in the phyloseq package. |
| 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. |
| refseq-method | Retrieve reference sequences ('XStringSet'-class) from object. |
| rm_outlierf | Set to FALSE any outlier species greater than f fractional abundance. |
| samData | Depcrecated functions in the phyloseq package. |
| sample.names | Depcrecated functions in the phyloseq package. |
| sample.variables | Depcrecated functions in the phyloseq package. |
| sampleData | Depcrecated functions in the phyloseq package. |
| sampleData<- | Depcrecated functions in the phyloseq package. |
| sampleNames | Depcrecated functions in the phyloseq package. |
| sampleSums | Depcrecated functions in the phyloseq package. |
| sample_data | Build or access sample_data. |
| sample_data-class | The S4 for storing sample variables. |
| sample_data-method | Build or access sample_data. |
| sample_data<- | Assign (new) sample_data to 'x' |
| sample_names | Get sample names. |
| sample_names-method | Get sample names. |
| sample_names<- | Replace OTU identifier names |
| sample_names<--method | 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 |
| sam_data | Depcrecated functions in the phyloseq package. |
| sam_data<- | Depcrecated functions in the phyloseq package. |
| show-method | method extensions to show for phyloseq objects. |
| show_mothur_cutoffs | Show cutoff values available in a mothur file. |
| show_mothur_list_cutoffs | Depcrecated functions in the phyloseq package. |
| soilrep | (Data) Reproducibility of soil microbiome data (2011) |
| species.names | Depcrecated functions in the phyloseq package. |
| speciesAreRows | Depcrecated functions in the phyloseq package. |
| speciesarerows | Depcrecated functions in the phyloseq package. |
| speciesAreRows<- | Depcrecated functions in the phyloseq package. |
| speciesSums | Depcrecated functions in the phyloseq package. |
| subset_ord_plot | Subset points from an ordination-derived ggplot |
| subset_samples | Subset samples by sample_data expression |
| subset_species | Depcrecated functions in the phyloseq package. |
| subset_taxa | Subset species by taxonomic expression |
| t | Transpose 'otu_table-class' or 'phyloseq-class' |
| t-method | Transpose 'otu_table-class' or 'phyloseq-class' |
| taxaplot | Depcrecated functions in the phyloseq package. |
| taxa_are_rows | Access taxa_are_rows slot from otu_table objects. |
| taxa_are_rows-method | Access taxa_are_rows slot from otu_table objects. |
| taxa_are_rows<- | Manually change taxa_are_rows through assignment. |
| taxa_are_rows<--method | Manually change taxa_are_rows through assignment. |
| taxa_names | Get species / taxa names. |
| taxa_names-method | Get species / taxa names. |
| taxa_names<- | Replace OTU identifier names |
| taxa_names<--method | Replace OTU identifier names |
| taxa_sums | Returns the total number of individuals observed from each species/taxa/OTU. |
| taxglom | Depcrecated functions in the phyloseq package. |
| taxonomyTable-class | An S4 class that holds taxonomic classification data as a character matrix. |
| taxTab | Depcrecated functions in the phyloseq package. |
| taxtab | Depcrecated functions in the phyloseq package. |
| taxTab<- | Depcrecated functions in the phyloseq package. |
| tax_glom | Agglomerate taxa of the same type. |
| tax_table | Build or access the taxonomyTable. |
| tax_table-method | Build or access the taxonomyTable. |
| tax_table<- | Assign a (new) Taxonomy Table to 'x' |
| tax_table<--method | Assign a (new) Taxonomy Table to 'x' |
| threshrank | Thresholded rank transformation. |
| threshrankfun | A closure version of the 'threshrank' function. |
| tipglom | Depcrecated functions in the phyloseq package. |
| 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 |
| transformSampleCounts | Transform abundance data in an 'otu_table', sample-by-sample. |
| transform_sample_counts | Transform abundance data in an 'otu_table', sample-by-sample. |
| tre | Depcrecated functions in the phyloseq package. |
| tre<- | Depcrecated functions in the phyloseq package. |
| tree_layout | Returns a data table defining the line segments of a phylogenetic tree. |
| UniFrac | Calculate weighted or unweighted (Fast) UniFrac distance for all sample pairs. |
| UniFrac-method | Calculate weighted or unweighted (Fast) UniFrac distance for all sample pairs. |
| [-method | Method extensions to extraction operator for phyloseq objects. |