Microbiome16S – Local 16S Microbiome Analysis App (QIIME2 → Publication Figures, Stats & Methods)

From QIIME2 artifacts to publication-ready figures, statistics and a paste-ready Methods paragraph – in minutes, with a point-and-click interface. Your data never leave your computer.

Handles repeated measures correctly: no pseudo-replication, no inflated p-values.

Stop fighting R scripts. Click, run, publish.

This Microbiome16S app digital product (a zip file) is a desktop app for downstream 16S rRNA analysis. It opens in your browser but runs 100% on your own computer, built on established R packages (phyloseq, vegan), tested with null simulations and spiked datasets (phyloseq + vegan).

How it works

1. Load your data: QIIME2 .qza files (no QIIME2 installation needed), or CSV/TSV/BIOM tables from any pipeline.
2. Choose your groups and rarefaction depth. You see live how many samples each group keeps.
3. Click Run.
4. Download figures, tables, an HTML report and your Methods text.

What you get from every run

• Publication-ready figures (PNG 300 dpi + editable vector PDF)
• A CSV table for every statistical test
• A self-contained HTML report to share with your PI or co-authors
• A Methods paragraph written from your actual parameters, with references
• phyloseq objects (.rds) to continue in R

Is it right for your study?

✅ One categorical grouping variable (2+ groups, ≥3 samples each)

✅ Independent samples or repeated measures (subject as blocking variable: every test respects it)

❌ Covariate adjustment, multi-factor or longitudinal models

❌ Confirmatory differential abundance (use ANCOM-BC2 / ALDEx2 / MaAsLin2 to confirm hits)

❌ Shotgun, ITS/18S, decontamination, batch correction

Analyses included

• QC & rarefaction: removal of mitochondria, chloroplasts and unassigned features; rarefaction curves
• Taxonomic composition: phylum and genus bar plots, per-taxon group tests with FDR
• Alpha diversity: Observed, Shannon, Gini-Simpson, Pielou, Faith PD, with significance brackets
• Beta diversity: Jaccard, Bray-Curtis, unweighted and weighted UniFrac; PCoA and NMDS; PERMANOVA (with blocking for repeated measures), pairwise PERMANOVA, dispersion tests
• Exploratory Differential abundance: two complementary approaches (relative abundance + CLR), with consensus hits highlighted
• Logistic regression: odds ratios with separation detection, cross-validated ROC/AUC
• Spearman correlations: genera vs. numeric metadata, global FDR heatmap

See how it works:

• Demo analysis included with QIIME2 "Moving Pictures" tutorial dataset.
• Exploratory analyses are clearly labelled as such in figures and Methods.

Private by design

No cloud, no uploads, no account. All analyses on your own computer.

Requirements

• macOS (Apple Silicon or Intel) or Linux
• R ≥ 4.1 and Python ≥ 3.9 (both free)
• On Mac: double-click installer. The required R packages install automatically.
• Windows is not officially supported yet.

License

Individual license for one user. Lab license available for up to 5 members of the same research group. Results, figures and reports are yours to publish.

Included

• Mac installer
• Installable app package
• README with installation guide and troubleshooting
• Example report