MicrobiomeAnalyst is a user-friendly, comprehensive web-based tool for analyzing data sets generated from microbiome studies (16S rRNA, metagenomics or metatranscriptomics data). The focus of this tool is to perform statistical analysis, visual exploration, and data integration. It is designed to support four kinds of analysis:
- Compositional profiling: (16S rRNA marker gene data) provides various common statistical methods for alpha and beta diversity analysis, coupled with different types of visualization support (bar charts, stacked area plots and pie-charts) to help users obtain a comprehensive view of the composition of their uploaded microbial communities.
- Functional profiling: (16S rRNA data) supports the prediction of metabolic potentials; (shotgun metagenomics or metatranscriptomics data) supports direct functional profiling at various levels: metabolic modules, metabolic pathways or higher functional (COG or EC) levels.
- Comparative analysis: supporting multiple data filtering and normalization techniques coupled with differential analysis methods (LEfSE, metagenomeSeq, edgeR, DEseq2, etc) to identify features that are significantly different between conditions under study.
- Meta analysis: allows users to directly compare their data sets with published human microbiome data in the projection with public data module (PPD), or compare important features with those defined or identified from literature or public resources in the taxon set enrichment analysis (TSEA) module.