Overview

What Microbiome Studio does

Microbiome Studio analyses amplicon feature tables with the methods microbial ecologists rely on: alpha diversity, Bray–Curtis and weighted or unweighted UniFrac distances, PCoA ordination, PERMANOVA tests and rarefaction curves.

Differential abundance uses centred log-ratio transformation, which respects the compositional nature of sequencing data.

Technical specifications

Inputs: Feature table · Sample metadata · Newick tree (optional)
Outputs: Diversity tables · Ordination plots · PERMANOVA results · DA tables
Engine: TypeScript kernels in a Web Worker
Platforms: Chrome, Edge, Firefox and Safari (current versions) · Windows, macOS, Linux and ChromeOS · No installation, no account, no upload
Limits: Amplicon-scale feature tables
Licence: Free during the public preview; institutional licences on request

Features

Capabilities

01

Alpha and beta diversity

Richness, Shannon and Simpson; Bray–Curtis and Jaccard distances.

02

UniFrac

Weighted and unweighted UniFrac with a phylogenetic tree.

03

Ordination and tests

PCoA with PERMANOVA on any metadata variable.

04

Compositional DA

CLR-based differential abundance.

05

Rarefaction

Curves to judge sequencing depth.

Use cases

Who uses it, and for what

Comparing microbial communities between conditions
Teaching microbiome analysis
Quick exploration before a QIIME 2 workflow

Documentation

Quick start

Open Microbiome Studio
Use the button on this page or the Workbench menu. Nothing to install; works in current Chrome, Edge, Firefox and Safari.
Load data or the demo
Drop in your files (Feature table, Sample metadata, Newick tree (optional)) or load the labelled synthetic demo to explore safely.
Run and inspect
Results appear as interactive figures and tables; each analysis records its parameters and versions.
Export and cite
Export figures and tables, add them to a report, and copy the auto-written methods paragraph.

Full documentation

Learn the methods with Vedicgen