Starting from marker gene abundance data (OTU/ASV table, BIOM file, mothur output)
Visually exploring your 16S rRNA data with a public data in a 3D PCoA plot
Starting from gene list or gene abundance data annotated by KO, EC or COG
Starting with a list of taxa of interest (strains, species or higher level taxa)


Marker Data Profiling (MDP): Comprehensive composition & diversity analysis supporting various methods of data overview, alpha diversity and beta-diversity; comparative analysis supporting multiple differential abundance methods (metagenomeSeq, LEfSe, edgeR, DESeq2, etc.); as well as prediction of metabolic potentials.


Shotgun Data Profiling (SDP): Functional diversity profiling based on KEGG annotations (modules, pathways, metabolisms), EC numbers, or COG categories, direct functional association testing, as well as differential abundance analysis followed by functional enrichment analysis within a powerful metabolic network visualization system.


Taxon Set Enrichment Analysis (TSEA): Enrichment analysis using ~2400 manually collected taxon sets organized into 11 different categories. They are defined based on their shared phenotypic traits or ecological niches, or their associations with host genetic variations, lifestyles, biochemistry, diseases, developmental stages, etc.


Projection with Public Data (PPD): Co-processing your data together with a suitable public 16S rRNA data of interest and explore the results within an interactive 3D PCoA visualization system to easily discover patterns of interest as well as to associate these patterns with underlying taxonomic variations.

News & Updates

  • Nature Protocols on MicrobiomeAnalyst is now released;
  • Enhanced correlation network visualization to display abundance piechart (02/12/2020);
  • Updated graph summary for Correlation network, and added SparCC correlation in Pattern Hunter (02/03/2020);
  • Code refactoring for better performance (01/08/2020);
  • Added support for prepending higher taxonomic levels for stacked bar/area plots (12/06/2019);
  • Fixed meta-data update issue after editing data (11/21/2019);
  • Added support for zip file upload (11/18/2019);
  • Stacked area plot now supports grouping (faceting) based on two factors (10/24/2019);
  • Updated R from 3.5.1 to the latest version (3.6.1) (10/16/2019);
  • Fixed the issue with core microbiome analysis (09/18/2019);
Read more ......

Please Cite

  • Chong, J., Liu, P., Zhou, G., and Xia. J. (2020) "Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data" Nature Protocols (DOI: 10.1038/s41596-019-0264-1)
  • Dhariwal, A., Chong, J., Habib, S., King, I., Agellon, LB., and Xia. J. (2017) "MicrobiomeAnalyst - a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data"
    Nucleic Acids Research 45 W180-188 (DOI: 10.1093/nar/gkx295)


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