TaxSEA: Taxon Set Enrichment Analysis | Installation | Taxon set database | Test data | Functions | Usage | Retrieve sets containing a particular taxon | Running an enrichment analysis | Run TaxSEA with test data | Output | BugSigDB | TaxSEA database with other enrichment tools

Why per-person enrichment? | How it works | Usage | From a count matrix | A single sample | With the built-in database | From a TreeSummarizedExperiment | Interpreting the scores | Practical considerations | When to use ssTaxSEA vs TaxSEA | Downstream analysis

The challenge with interpreting differences in microbiome data | The idea behind Taxon Set Enrichment Analysis | But isn’t this what functional profiling tools (e.g. HUMAnN3) do?

ORA vs Enrichment (two ways to run TaxSEA) | Enrichment (rank-based) | What it does (in plain terms) | When to use it (recommended in most cases) | Pros | Cons | ORA (Over-Representation Analysis) | When to use it | Recommended practice

What problem does TaxSEA actually solve? | Is TaxSEA a replacement for differential abundance? | Can I use TaxSEA even when there are no individual species level differences? | How is this different from functional profiling tools like HUMAnN3? | Does this only work for the human gut microbiome? | Do I need differential abundance results first? | Why use ranks instead of thresholds? | Isn’t this just gene set enrichment, but for microbes? | Will this work if my DA results are messy or inconsistent? | Have you shown TaxSEA is accurate? | When should I not use TaxSEA? | Can I use TaxSEA with 16S rRNA gene sequencing data? | Why does TaxSEA use species-level data instead of strain-level?