Load your feature table, taxonomy and metadata, pick a grouping variable, click Run. Get publication-ready figures, full statistics, an HTML report and a paste-ready Methods paragraph in minutes. Everything runs on your computer.
One-time purchase. Download and use, no account.
Real output on the QIIME2 Moving Pictures dataset (Caporaso et al., 2011).
Microbiome16S is a local app. The interface opens in your browser, but the server is your own machine. No uploads, no accounts, no cloud processing. That makes it a safe choice for unpublished, clinical or embargoed datasets.
Network use: only the one-time installation of R packages.
The app walks you through the same order every time, so every run is documented and repeatable.
Drop in QIIME2 artifacts or plain tables, or point to paths on your computer for large files. Orientation, prefixes like k__ and #q2:types rows are handled for you. A recap shows samples, features and sequencing depth before you go on.
Choose the grouping variable, an optional blocking factor (e.g. subject) and the rarefaction depth, with a preview of how many samples each group keeps. Advanced parameters are there when you need them.
One click runs QC, diversity, statistics, differential abundance, regression and correlations. A live log shows each step.
Read the key results at a glance, open the comprehensive HTML report, copy the Methods text, or download everything as one ZIP.
Seven modules, run with established R packages and documented defaults.
Removes unassigned, mitochondrial and chloroplast features. Depth chooser with per-group retention, seeded rarefaction without replacement, rarefaction curves.
Phylum and genus bar plots per sample and per group. Wilcoxon or Kruskal-Wallis per taxon with BH correction.
Observed, Shannon, Gini-Simpson, Pielou and Faith PD (with a tree). Wilcoxon or Kruskal-Wallis with η²[H], Dunn (BH) brackets.
Jaccard, Bray-Curtis, unweighted and weighted UniFrac. PCoA and NMDS, PERMANOVA with optional blocking, betadisper, pairwise PERMANOVA (BH).
Genus level, tested on relative abundance and on CLR. Consensus hits, volcano and ranking plots, Dunn post-hoc.
Univariate models on standardised CLR, odds ratios with 95% CI, separation detection, repeated stratified cross-validated AUC.
Spearman between CLR genera and numeric metadata, with one global BH-FDR correction and a heatmap.
phyloseq::UniFrac() gives wrong distances on trees with polytomies, common with FastTree. Microbiome16S resolves them first and was verified against an independent implementation.
Differential abundance by rank tests is labelled exploratory, consensus hits are reported, and the Methods text says when AUC may be optimistic.
Each run gets its own dated folder, so you can compare settings and always know which figure came from which parameters.
“Samples were rarefied without replacement to 1,103 reads per sample (random seed 42); 31 of 34 samples were retained… Group differences were tested by PERMANOVA (vegan::adonis2, 999 permutations, permutations restricted within levels of ‘subject’)…”
Numbers, groups and options are filled in automatically. No brackets to edit.
Same validated statistics as our R workflow, without the RStudio sessions.
On a Mac, double-click Install Microbiome16S.command. It creates a private environment, installs the R packages (5–20 minutes the first time) and puts a Start icon on your Desktop.
microbiome16s # open the app at localhost:8516 microbiome16s doctor # check R and packages (--install to fix) microbiome16s demo # download the Moving Pictures test data microbiome16s run --table table.qza --taxonomy taxonomy.qza \ --metadata metadata.tsv --tree rooted-tree.qza --group body-site --strata subject
Self-service tool sold as is: no account, no subscription.
For one researcher
One-time purchase · instant download
For one research group, up to 5 users
One-time purchase · instant download
Install once, then go from feature table to figures, statistics and Methods text in a single run, on your own computer.
Download the App for $34.99One-time purchase. Self-service, sold as is.