Paul J. McMurdie & Joseph N. Paulson | phyloseq Home Page | Motivation for the biomformat package | Read BIOM format | Access BIOM data | Core observation data | Observation Metadata | Sample Metadata | Plots | Write BIOM format (JSON / v1) | HDF5 (BIOM v2) read and write | Tidy long-format output | purrr-style summarisation over samples | SummarizedExperiment interoperability | Constructing a BIOM from R data | Subsetting biom_data() by name | Session info

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

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

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 (Modern) | Sample data from QIIME | Input | Output | QIIME Example Tutorial | Import from QIIME Legacy | Import from mothur | Import from PyroTagger | Import from RDP pipeline | Expected Naming Convention | Example Data (included) | phyloseq Object Summaries | Convert raw data to phyloseq components | phyloseq() function: building complex phyloseq objects | Merge | Accessor functions | Trimming, subsetting, filtering phyloseq data | Trimming: prune_taxa() | Simple filtering example | Arbitrarily complex abundance filtering | genefilter_sample(): Filter by Within-Sample Criteria | filter_taxa(): Filter by Across-Sample Criteria | subset_samples(): Subset by Sample Variables | subset_taxa(): subset by taxonomic categories | random subsample abundance data | Transform abundance data | Phylogenetic smoothing | tax_glom() | tip_glom() | Installation | Installing Parallel Backend | References

- 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)