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"otu_table<-,phyloseq,phyloseq-method" ] }, { "page": "parseTaxonomy-functions", "title": "Parse elements of a taxonomy vector", "topics": [ "parse_taxonomy_default", "parse_taxonomy_greengenes", "parse_taxonomy_qiime" ] }, { "page": "phy_tree-methods", "title": "Retrieve phylogenetic tree ('phylo'-class) from object.", "topics": [ "phy_tree", "phy_tree,ANY-method", "phy_tree,phylo-method" ] }, { "page": "assign-phy_tree", "title": "Assign a (new) phylogenetic tree to 'x'", "topics": [ "assign-phy_tree", "phy_tree<-", "phy_tree<-,phyloseq,phylo-method", "phy_tree<-,phyloseq,phyloseq-method" ] }, { "page": "phylo-class", "title": "An S4 placeholder of the main phylogenetic tree class from the ape package.", "topics": [ "phylo-class" ] }, { "page": "phyloseq", "title": "Build phyloseq-class objects from their components.", "topics": [ "phyloseq" ] }, { "page": "phyloseq_to_deseq2", "title": "Convert phyloseq data to DESeq2 dds object", "topics": [ "phyloseq_to_deseq2" ] }, { "page": "phyloseq_to_metagenomeSeq", "title": "Convert phyloseq data to MetagenomeSeq MRexperiment object", "topics": [ "phyloseq_to_metagenomeSeq" ] }, { "page": "phyloseq-class", "title": "The main experiment-level class for phyloseq data", "topics": [ "phyloseq-class" ] }, { "page": "phyloseq-deprecated", "title": "Depcrecated functions in the phyloseq package.", "topics": [ "deprecated_phyloseq_function", "filterfunSample", "genefilterSample", "getSamples", "getSpecies", "getTaxa", "getVariable", "import_qiime_sampleData", "merge_species", "nspecies", "otuTable", "otuTable<-", "phyloseq-deprecated", "plot_richness_estimates", "plot_taxa_bar", "prune_species", "rank.names", "samData", "sample.names", "sample.variables", "sampleData", "sampleData<-", "sampleNames", "sampleSums", "sam_data", "sam_data<-", "show_mothur_list_cutoffs", "species.names", "speciesAreRows", "speciesarerows", "speciesAreRows<-", "speciesSums", "subset_species", "taxaplot", "taxglom", "taxTab", "taxtab", "taxTab<-", "tipglom", "tre", "tre<-" ] }, { "page": "plot_bar", "title": "A flexible, informative barplot phyloseq data", "topics": [ "plot_bar" ] }, { "page": "plot_clusgap", "title": "Create a ggplot summary of gap statistic results", "topics": [ "plot_clusgap" ] }, { "page": "plot_heatmap", "title": "Create an ecologically-organized heatmap using ggplot2 graphics", "topics": [ "plot_heatmap" ] }, { "page": "plot_net", "title": "Microbiome Network Plot using ggplot2", "topics": [ "plot_net" ] }, { "page": "plot_network", "title": "Microbiome Network Plot using ggplot2", "topics": [ "plot_network" ] }, { "page": "plot_ordination", "title": "General ordination plotter based on ggplot2.", "topics": [ "plot_ordination" ] }, { "page": "plot_phyloseq-methods", "title": "Generic plot defaults for phyloseq.", "topics": [ "plot_phyloseq", "plot_phyloseq,phyloseq-method" ] }, { "page": "plot_richness", "title": "Plot alpha diversity, flexibly with ggplot2", "topics": [ "plot_richness" ] }, { "page": "plot_scree", "title": "General ordination eigenvalue plotter using ggplot2.", "topics": [ "plot_scree" ] }, { "page": "plot_tree", "title": "Plot a phylogenetic tree with optional annotations", "topics": [ "plot_tree" ] }, { "page": "prune_samples-methods", "title": "Define a subset of samples to keep in a phyloseq object.", "topics": [ "prune_samples", "prune_samples,character,otu_table-method", "prune_samples,character,phyloseq-method", "prune_samples,character,sample_data-method", "prune_samples,logical,ANY-method" ] }, { "page": "prune_taxa-methods", "title": "Prune unwanted OTUs / taxa from a phylogenetic object.", "topics": [ "prune_taxa", "prune_taxa,character,otu_table-method", "prune_taxa,character,phylo-method", "prune_taxa,character,phyloseq-method", "prune_taxa,character,sample_data-method", "prune_taxa,character,taxonomyTable-method", "prune_taxa,character,XStringSet-method", "prune_taxa,logical,ANY-method", "prune_taxa,NULL,ANY-method" ] }, { "page": "psmelt", "title": "Melt phyloseq data object into large data.frame", "topics": [ "psmelt" ] }, { "page": "rank_names", "title": "Retrieve the names of the taxonomic ranks", "topics": [ "rank_names" ] }, { "page": "rarefy_even_depth", "title": "Resample an OTU table such that all samples have the same library size.", "topics": [ "rarefy_even_depth" ] }, { "page": "read_tree", "title": "Somewhat flexible tree-import function", "topics": [ "read_tree" ] }, { "page": "read_tree_greengenes", "title": "Read GreenGenes tree released in annotated newick format", "topics": [ "read_tree_greengenes" ] }, { "page": "refseq-methods", "title": "Retrieve reference sequences ('XStringSet'-class) from object.", "topics": [ "refseq", "refseq,ANY-method", "refseq,XStringSet-method" ] }, { "page": "rm_outlierf", "title": "Set to FALSE any outlier species greater than f fractional abundance.", "topics": [ "rm_outlierf" ] }, { "page": "sample_data-methods", "title": "Build or access sample_data.", "topics": [ "sample_data", "sample_data,ANY-method", "sample_data,data.frame-method" ] }, { "page": "sample_data-class", "title": "The S4 for storing sample variables.", "topics": [ "sample_data-class" ] }, { "page": "assign-sample_data", "title": "Assign (new) sample_data to 'x'", "topics": [ "assign-sample_data", "sample_data<-" ] }, { "page": "sample_names-methods", "title": "Get sample names.", "topics": [ "sample_names", "sample_names,ANY-method", "sample_names,otu_table-method", "sample_names,phyloseq-method", "sample_names,sample_data-method" ] }, { "page": "assign-sample_names", "title": "Replace OTU identifier names", "topics": [ "assign-sample_names", "sample_names<-", "sample_names<-,ANY,ANY-method", "sample_names<-,ANY,character-method", "sample_names<-,otu_table,character-method", "sample_names<-,phyloseq,character-method", "sample_names<-,sample_data,character-method" ] }, { "page": "sample_sums", "title": "Returns the total number of individuals observed from each sample.", "topics": [ "sample_sums" ] }, { "page": "sample_variables", "title": "Get the sample variables present in sample_data", "topics": [ "sample_variables" ] }, { "page": "show_mothur_cutoffs", "title": "Show cutoff values available in a mothur file.", "topics": [ "show_mothur_cutoffs" ] }, { "page": "show-methods", "title": "method extensions to show for phyloseq objects.", "topics": [ "show,otu_table-method", "show,phyloseq-method", "show,sample_data-method", "show,taxonomyTable-method" ] }, { "page": "subset_ord_plot", "title": "Subset points from an ordination-derived ggplot", "topics": [ "subset_ord_plot" ] }, { "page": "subset_samples-methods", "title": "Subset samples by sample_data expression", "topics": [ "subset_samples" ] }, { "page": "subset_taxa-methods", "title": "Subset species by taxonomic expression", "topics": [ "subset_taxa" ] }, { "page": "transpose-methods", "title": "Transpose 'otu_table-class' or 'phyloseq-class'", "topics": [ "t", "t,otu_table-method", "t,phyloseq-method" ] }, { "page": "tax_glom", "title": "Agglomerate taxa of the same type.", "topics": [ "tax_glom" ] }, { "page": "tax_table-methods", "title": "Build or access the taxonomyTable.", "topics": [ "tax_table", "tax_table,ANY-method", "tax_table,data.frame-method", "tax_table,matrix-method" ] }, { "page": "assign-tax_table", "title": "Assign a (new) Taxonomy Table to 'x'", "topics": [ "assign-tax_table", "tax_table<-", "tax_table<-,phyloseq,ANY-method", "tax_table<-,phyloseq,taxonomyTable-method", "tax_table<-,taxonomyTable,ANY-method", "tax_table<-,taxonomyTable,taxonomyTable-method" ] }, { "page": "taxa_are_rows-methods", "title": "Access taxa_are_rows slot from otu_table objects.", "topics": [ "taxa_are_rows", "taxa_are_rows,ANY-method", "taxa_are_rows,otu_table-method", "taxa_are_rows,phyloseq-method" ] }, { "page": "assign-taxa_are_rows", "title": "Manually change taxa_are_rows through assignment.", "topics": [ "assign-taxa_are_rows", "taxa_are_rows<-", "taxa_are_rows<-,otu_table,logical-method", "taxa_are_rows<-,phyloseq,logical-method" ] }, { "page": "taxa_names-methods", "title": "Get species / taxa names.", "topics": [ "taxa_names", "taxa_names,ANY-method", "taxa_names,otu_table-method", "taxa_names,phylo-method", "taxa_names,phyloseq-method", "taxa_names,sample_data-method", "taxa_names,taxonomyTable-method", "taxa_names,XStringSet-method" ] }, { "page": "assign-taxa_names", "title": "Replace OTU identifier names", "topics": [ "assign-taxa_names", "taxa_names<-", "taxa_names<-,ANY,ANY-method", "taxa_names<-,ANY,character-method", "taxa_names<-,otu_table,character-method", "taxa_names<-,phylo,character-method", "taxa_names<-,phyloseq,character-method", "taxa_names<-,taxonomyTable,character-method", "taxa_names<-,XStringSet,character-method" ] }, { "page": "taxa_sums", "title": "Returns the total number of individuals observed from each species/taxa/OTU.", "topics": [ "taxa_sums" ] }, { "page": "taxonomyTable-class", "title": "An S4 class that holds taxonomic classification data as a character matrix.", "topics": [ "taxonomyTable-class" ] }, { "page": "threshrank", "title": "Thresholded rank transformation.", "topics": [ "threshrank" ] }, { "page": "threshrankfun", "title": "A closure version of the 'threshrank' function.", "topics": [ "threshrankfun" ] }, { "page": "tip_glom", "title": "Agglomerate closely-related taxa using single-linkage clustering.", "topics": [ "tip_glom" ] }, { "page": "topf", "title": "Make filter fun. that returns the top f fraction of taxa in a sample.", "topics": [ "topf" ] }, { "page": "topk", "title": "Make filter fun. the most abundant 'k' taxa", "topics": [ "topk" ] }, { "page": "topp", "title": "Make filter fun. that returns the most abundant 'p' fraction of taxa", "topics": [ "topp" ] }, { "page": "transformcounts", "title": "Transform abundance data in an 'otu_table', sample-by-sample.", "topics": [ "transformSampleCounts", "transform_sample_counts" ] }, { "page": "tree_layout", "title": "Returns a data table defining the line segments of a phylogenetic tree.", "topics": [ "tree_layout" ] }, { "page": "UniFrac-methods", "title": "Calculate weighted or unweighted (Fast) UniFrac distance for all sample pairs.", "topics": [ "UniFrac", "UniFrac,phyloseq-method" ] } ], "_readme": "https://github.com/bioc/phyloseq/raw/HEAD/README.md", "_rundeps": [ "ade4", "ape", "Biobase", "BiocGenerics", "biomformat", "Biostrings", "cli", "cluster", "codetools", "cpp11", "crayon", "data.table", "digest", "farver", "foreach", "generics", "ggplot2", "glue", "gtable", "igraph", "IRanges", "isoband", "iterators", "jsonlite", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "mgcv", "multtest", "nlme", "permute", "pixmap", "pkgconfig", "plyr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "reshape2", "rlang", "S4Vectors", "S7", "scales", "Seqinfo", "sp", "stringi", "stringr", "survival", "vctrs", "vegan", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "phyloseq-analysis.Rmd", "filename": "phyloseq-analysis.html", "title": "Vignette for phyloseq: Analysis of high-throughput microbiome census data", "engine": "knitr::rmarkdown", "headings": [ "Other resources", "Summary", "About this vignette", "Data", "Interface with the microbio.me/qiime server", "Included Data", "Simple exploratory graphics", "Easy Richness Estimates", "Exploratory tree plots", "Exploratory bar plots", "Exploratory analysis and graphics", "Exploratory Heat Map", "Microbiome Network Representation", "Ordination Methods", "Principal Coordinates Analysis (PCoA)", "non-metric Multi-Dimensional Scaling (NMDS)", "Correspondence Analysis (CA)", "Double Principle Coordinate Analysis (DPCoA)", "Distance Methods", "distance(): Central Distance Function", "UniFrac and weighted UniFrac", "Hierarchical Clustering", "Multiple Testing and Differential Abundance" ], "created": "2013-10-16 19:02:13", "modified": "2026-02-27 23:49:05", "commits": 12 }, { "source": "phyloseq-mixture-models.Rmd", "filename": "phyloseq-mixture-models.html", "title": "Example using Negative Binomial in Microbiome Differential Abundance Testing", "engine": "knitr::rmarkdown", "headings": [ "Other resources", "The experimental data used in this example", "Import data with phyloseq, convert to DESeq2", "Convert to DESeq2's DESeqDataSet class", "DESeq2 conversion and call", "Investigate test results table", "Plot Results" ], "created": "2013-10-24 00:00:45", "modified": "2026-02-27 23:49:05", "commits": 9 }, { "source": "phyloseq-basics.Rmd", "filename": "phyloseq-basics.html", "title": "Basic storage, access, and manipulation of phylogenetic sequencing data with phyloseq", "engine": "knitr::rmarkdown", "headings": [ "Other resources", "Introduction", "About this vignette", "Typesetting Legend ", "Other links and tutorials", "phyloseq classes ", "Load phyloseq and import data ", "Load phyloseq", "Import data", "Import from biom-format ", "Import from QIIME 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23:49:05", "commits": 5 }, { "source": "phyloseq-FAQ.Rmd", "filename": "phyloseq-FAQ.html", "title": "phyloseq Frequently Asked Questions (FAQ)", "author": "Paul McMurdie and Susan Holmes", "engine": "knitr::rmarkdown", "headings": [ "- I tried reading my biom file using phyloseq, but it didn’t work. What’s wrong?", "Good News: HDF5-biom should be supported in next release", "HDF5 (Version 2.0) biom-format: biomformat", "Not every data component is included in .biom files", "Other issues related the biom-format", "- microbio_me_qiime() returned an error. What’s wrong?", "The QIIME-DB Server is Permanently Down.", "An interface to Qiita is Planned.", "- I want a phyloseq graphic that looks like...", "Modify the ggplot object yourself.", "psmelt and ggplot2", "Submit a Pull Request (Advanced)", "Define a ggplot2 extension (Advanced)", "- There’s a typo in phyloseq documentation, tutorials, or vignettes", "Fix the typo directly on GitHub", "Minimal GIT and GitHub Exercise", "- I read \"Waste Not, Want Not...\" but...", "I tried to use DESeq2 to normalize my data, but now I don't know what to do...", "My libraries/samples had different total number of reads, what do I do?", "Should I normalize my data before alpha-diversity analysis", "Negative numbers in my transformed data table?", "I get an error regarding geometric mean", "Pseudocounts are not appropriate for my data, because...", "I’m scared that the Negative Binomial doesn’t fit my data well", "I don’t know how to test for differential abundance now. How do I do that?", "- I need help analyzing my data. It has the following study design...", "Please be more specific", "Please respect my time (and other package authors)", "Pay for Help (not me)" ], "created": "2016-03-23 00:14:21", "modified": "2019-02-17 22:28:11", "commits": 3 } ], "_score": 16.149343855989088, "_indexed": true, "_nocasepkg": "phyloseq", "_universes": [ "bioc", "joey711" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.57.0", "date": "2026-05-30T07:17:45.000Z", "distro": "noble", "commit": "c9fa4810a72c15e963c248b4c6acec693d7757f9", "fileid": "1538e6be5b04e3db27d8fcfc9bd9e16c740812321a8dfd4e911fe80d6e5d5f1c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677685447" }, { "r": "4.6.0", "os": "linux", "version": "1.57.0", "date": "2026-05-30T07:20:06.000Z", "distro": "noble", "commit": "c9fa4810a72c15e963c248b4c6acec693d7757f9", "fileid": "a107910dae0976fa60c2a6ec62e98140bc1bb46da303416c91a31c215d0b93f9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677685447" }, { "r": "4.5.3", "os": "mac", "version": "1.57.0", "date": "2026-05-30T10:06:27.000Z", "commit": "c9fa4810a72c15e963c248b4c6acec693d7757f9", "fileid": "fb394237e76dd0dad3bbfbdd9b8b4e61622879daf1d5f5c6e23c86a09aecb35a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677685447" }, { "r": "4.6.0", "os": "mac", "version": "1.57.0", "date": "2026-05-30T10:05:18.000Z", "commit": "c9fa4810a72c15e963c248b4c6acec693d7757f9", "fileid": "ca40638534ff32af9874cce1364d7c39e9ae0ede044310735220091a0d8bf6e9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677685447" }, { "r": "4.6.0", "os": "wasm", "version": "1.57.0", "date": "2026-05-30T07:17:24.000Z", "commit": "c9fa4810a72c15e963c248b4c6acec693d7757f9", "fileid": "0d4aeb30ef92328c35f158cd11fda4a4e4d425f4d4d80c4eab757a31bd1b61ec", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677685447" }, { "r": "4.7.0", "os": "win", "version": "1.57.0", "date": "2026-05-30T07:21:44.000Z", "commit": "c9fa4810a72c15e963c248b4c6acec693d7757f9", "fileid": "3139ddebeb6b635fd1bf381278a1ac4af359d65822ec773d8b8b17b2c0536339", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677685447" }, { "r": "4.5.3", "os": "win", "version": "1.57.0", "date": "2026-05-30T07:21:24.000Z", "commit": "c9fa4810a72c15e963c248b4c6acec693d7757f9", "fileid": "b23c805e2d892b87f7d28b87859cc5a6bb5a9116544034891dea240f758a8764", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677685447" }, { "r": "4.6.0", "os": "win", "version": "1.57.0", "date": "2026-05-30T07:16:26.000Z", "commit": "c9fa4810a72c15e963c248b4c6acec693d7757f9", "fileid": "a300689fd06356c46762e11a6bccabd53331b9a92e1c1409fc3eec04354ed1ca", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677685447" } ] }