SimpleMicrobiome enables key microbiome analyses and visualizations.
Start here:
Go to the
Data Loading
menu first.
Guide:
Open the user manual
here
.
Quick Workflow
- Data Loading: Upload feature table, taxonomy, and metadata.
- Preprocessing: Filter data by read counts and user-selected options.
- Analysis: Run Taxa Profiles/Diversity/DA/Network/Association modules as needed.
Version History
Show updates
- 260731: v0.4.6 - More reliable Docker dependency restoration with renv caching and retry support.
- 260728: v0.4.5 - Reproducible R 4.5.1 setup, dataset-aware taxonomic ranks, and run-consistent analysis outputs.
- 260708: v0.4.4 - Beta diversity NMDS run details and Docker-based local usage documentation.
- 260630: v0.4.3 - ANCOM-BC2/SparCC fixes, favicon fix, and manual documentation updates.
- 260629: v0.4.2 - R 4.5 installer updates, selectable example datasets, and Random Forest report text fixes.
- 260619: v0.4.1 - ANCOM-BC2 install compatibility and UI order updates.
- 260608: v0.4.0 - PNG export bug fixes.
- 260506: v0.3.0 - DA/Network/Association modules updated with new features and bug fixes.
- 260310: v0.2.0 - Preprocessing functionality improved.
- 251210: v0.1.0 - First version released.
© 2025-2026 SimpleMicrobiome | Microbial Genomics Lab
Contact: yongjoon (at) kangwon.ac.kr
Data Input
1. ASV/OTU Abundance Matrix
2. Taxonomy Table
3. Metadata Table
Example dataset
This tool requires 3 tsv files:
- ASV/OTU Abundance Matrix from table.qza of QIIME2
- Taxonomy table from taxonomy.qza of QIIME2
- Metadata table prepared manually by the user (see the example file)
- The first column should contain sample IDs, and its column name must be 'SampleID'.
To convert QZA files to input files, use QZA Converter
Sample Selection
Read Counts Filtering
Group-based Toggle
Individual Sample Selection (Click to Toggle)
After finishing selection, click another analysis tab to continue.
Taxa Comparison
Comparison Status
Alpha Diversity
Beta Diversity
Random Forest
Random Forest Status
SparCC Network
SparCC Status
SpiecEasi Network
SpiecEasi Status
Correlation Heatmap
Heatmap Status
Association Biplot
Biplot Status
Citation
References are grouped by module (APA style).